diff --git a/crates/ruff/src/importer/insertion.rs b/crates/ruff/src/importer/insertion.rs
index 469f7a1d28513..bb893822a05ea 100644
--- a/crates/ruff/src/importer/insertion.rs
+++ b/crates/ruff/src/importer/insertion.rs
@@ -302,7 +302,7 @@ mod tests {
     use ruff_text_size::TextSize;
     use rustpython_parser::ast::Suite;
     use rustpython_parser::lexer::LexResult;
-    use rustpython_parser::Parse;
+    use rustpython_parser::{Mode, Parse};
 
     use ruff_python_ast::source_code::{Locator, Stylist};
     use ruff_python_whitespace::LineEnding;
@@ -313,7 +313,7 @@ mod tests {
     fn start_of_file() -> Result<()> {
         fn insert(contents: &str) -> Result<Insertion> {
             let program = Suite::parse(contents, "<filename>")?;
-            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents);
+            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents, Mode::Module);
             let locator = Locator::new(contents);
             let stylist = Stylist::from_tokens(&tokens, &locator);
             Ok(Insertion::start_of_file(&program, &locator, &stylist))
@@ -424,7 +424,7 @@ x = 1
     #[test]
     fn start_of_block() {
         fn insert(contents: &str, offset: TextSize) -> Insertion {
-            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents);
+            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents, Mode::Module);
             let locator = Locator::new(contents);
             let stylist = Stylist::from_tokens(&tokens, &locator);
             Insertion::start_of_block(offset, &locator, &stylist)
diff --git a/crates/ruff/src/jupyter/notebook.rs b/crates/ruff/src/jupyter/notebook.rs
index 342bc249309b5..0bee249c95ff5 100644
--- a/crates/ruff/src/jupyter/notebook.rs
+++ b/crates/ruff/src/jupyter/notebook.rs
@@ -6,6 +6,7 @@ use std::path::Path;
 
 use itertools::Itertools;
 use once_cell::sync::OnceCell;
+use rustpython_parser::Mode;
 use serde::Serialize;
 use serde_json::error::Category;
 
@@ -151,7 +152,7 @@ impl Notebook {
                                 )
                             })?;
                             // Check if tokenizing was successful and the file is non-empty
-                            if (ruff_rustpython::tokenize(&contents))
+                            if (ruff_rustpython::tokenize(&contents, Mode::Module))
                                 .last()
                                 .map_or(true, Result::is_err)
                             {
diff --git a/crates/ruff/src/linter.rs b/crates/ruff/src/linter.rs
index ebdfded081327..b16ee6cb77c7a 100644
--- a/crates/ruff/src/linter.rs
+++ b/crates/ruff/src/linter.rs
@@ -8,7 +8,7 @@ use itertools::Itertools;
 use log::error;
 use rustc_hash::FxHashMap;
 use rustpython_parser::lexer::LexResult;
-use rustpython_parser::ParseError;
+use rustpython_parser::{Mode, ParseError};
 
 use ruff_diagnostics::Diagnostic;
 use ruff_python_ast::imports::ImportMap;
@@ -134,7 +134,12 @@ pub fn check_path(
             .iter_enabled()
             .any(|rule_code| rule_code.lint_source().is_imports());
     if use_ast || use_imports || use_doc_lines {
-        match ruff_rustpython::parse_program_tokens(tokens, &path.to_string_lossy()) {
+        let mode = if source_kind.map_or(false, |kind| kind.is_jupyter()) {
+            Mode::Jupyter
+        } else {
+            Mode::Module
+        };
+        match ruff_rustpython::parse_program_tokens(tokens, mode, &path.to_string_lossy()) {
             Ok(python_ast) => {
                 if use_ast {
                     diagnostics.extend(check_ast(
@@ -255,7 +260,7 @@ pub fn add_noqa_to_path(path: &Path, package: Option<&Path>, settings: &Settings
     let contents = std::fs::read_to_string(path)?;
 
     // Tokenize once.
-    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents);
+    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents, Mode::Module);
 
     // Map row and column locations to byte slices (lazily).
     let locator = Locator::new(&contents);
@@ -320,9 +325,16 @@ pub fn lint_only(
     package: Option<&Path>,
     settings: &Settings,
     noqa: flags::Noqa,
+    source_kind: Option<&SourceKind>,
 ) -> LinterResult<(Vec<Message>, Option<ImportMap>)> {
+    let mode = if source_kind.map_or(false, |source_kind| source_kind.is_jupyter()) {
+        Mode::Jupyter
+    } else {
+        Mode::Module
+    };
+
     // Tokenize once.
-    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents);
+    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents, mode);
 
     // Map row and column locations to byte slices (lazily).
     let locator = Locator::new(contents);
@@ -352,7 +364,7 @@ pub fn lint_only(
         &directives,
         settings,
         noqa,
-        None,
+        source_kind,
     );
 
     result.map(|(diagnostics, imports)| {
@@ -411,10 +423,16 @@ pub fn lint_fix<'a>(
     // Track whether the _initial_ source code was parseable.
     let mut parseable = false;
 
+    let mode = if source_kind.is_jupyter() {
+        Mode::Jupyter
+    } else {
+        Mode::Module
+    };
+
     // Continuously autofix until the source code stabilizes.
     loop {
         // Tokenize once.
-        let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&transformed);
+        let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&transformed, mode);
 
         // Map row and column locations to byte slices (lazily).
         let locator = Locator::new(&transformed);
diff --git a/crates/ruff/src/rules/pyflakes/mod.rs b/crates/ruff/src/rules/pyflakes/mod.rs
index e796ac45639fd..052fb4772f438 100644
--- a/crates/ruff/src/rules/pyflakes/mod.rs
+++ b/crates/ruff/src/rules/pyflakes/mod.rs
@@ -12,6 +12,7 @@ mod tests {
     use anyhow::Result;
     use regex::Regex;
     use rustpython_parser::lexer::LexResult;
+    use rustpython_parser::Mode;
     use test_case::test_case;
 
     use ruff_diagnostics::Diagnostic;
@@ -499,7 +500,7 @@ mod tests {
     fn flakes(contents: &str, expected: &[Rule]) {
         let contents = dedent(contents);
         let settings = Settings::for_rules(Linter::Pyflakes.rules());
-        let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents);
+        let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents, Mode::Module);
         let locator = Locator::new(&contents);
         let stylist = Stylist::from_tokens(&tokens, &locator);
         let indexer = Indexer::from_tokens(&tokens, &locator);
diff --git a/crates/ruff/src/test.rs b/crates/ruff/src/test.rs
index 1c2eb7aefb46a..995197abbf68b 100644
--- a/crates/ruff/src/test.rs
+++ b/crates/ruff/src/test.rs
@@ -9,6 +9,7 @@ use itertools::Itertools;
 use ruff_textwrap::dedent;
 use rustc_hash::FxHashMap;
 use rustpython_parser::lexer::LexResult;
+use rustpython_parser::Mode;
 
 use ruff_diagnostics::{AutofixKind, Diagnostic};
 use ruff_python_ast::source_code::{Indexer, Locator, SourceFileBuilder, Stylist};
@@ -97,8 +98,13 @@ pub(crate) fn max_iterations() -> usize {
 /// A convenient wrapper around [`check_path`], that additionally
 /// asserts that autofixes converge after a fixed number of iterations.
 fn test_contents(source_kind: &mut SourceKind, path: &Path, settings: &Settings) -> Vec<Message> {
+    let mode = if source_kind.is_jupyter() {
+        Mode::Jupyter
+    } else {
+        Mode::Module
+    };
     let contents = source_kind.content().to_string();
-    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents);
+    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&contents, mode);
     let locator = Locator::new(&contents);
     let stylist = Stylist::from_tokens(&tokens, &locator);
     let indexer = Indexer::from_tokens(&tokens, &locator);
@@ -160,7 +166,7 @@ fn test_contents(source_kind: &mut SourceKind, path: &Path, settings: &Settings)
                 notebook.update(&source_map, &fixed_contents);
             };
 
-            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&fixed_contents);
+            let tokens: Vec<LexResult> = ruff_rustpython::tokenize(&fixed_contents, mode);
             let locator = Locator::new(&fixed_contents);
             let stylist = Stylist::from_tokens(&tokens, &locator);
             let indexer = Indexer::from_tokens(&tokens, &locator);
diff --git a/crates/ruff_benchmark/benches/linter.rs b/crates/ruff_benchmark/benches/linter.rs
index 98ea5c1bd3327..7abaa4fdafa25 100644
--- a/crates/ruff_benchmark/benches/linter.rs
+++ b/crates/ruff_benchmark/benches/linter.rs
@@ -63,6 +63,7 @@ fn benchmark_linter(mut group: BenchmarkGroup<WallTime>, settings: &Settings) {
                         None,
                         settings,
                         flags::Noqa::Enabled,
+                        None,
                     );
 
                     // Assert that file contains no parse errors
diff --git a/crates/ruff_cli/src/diagnostics.rs b/crates/ruff_cli/src/diagnostics.rs
index f994b7a055e05..1d058b9b98ff1 100644
--- a/crates/ruff_cli/src/diagnostics.rs
+++ b/crates/ruff_cli/src/diagnostics.rs
@@ -204,12 +204,26 @@ pub(crate) fn lint_path(
             (result, fixed)
         } else {
             // If we fail to autofix, lint the original source code.
-            let result = lint_only(&contents, path, package, &settings.lib, noqa);
+            let result = lint_only(
+                &contents,
+                path,
+                package,
+                &settings.lib,
+                noqa,
+                Some(&source_kind),
+            );
             let fixed = FxHashMap::default();
             (result, fixed)
         }
     } else {
-        let result = lint_only(&contents, path, package, &settings.lib, noqa);
+        let result = lint_only(
+            &contents,
+            path,
+            package,
+            &settings.lib,
+            noqa,
+            Some(&source_kind),
+        );
         let fixed = FxHashMap::default();
         (result, fixed)
     };
@@ -316,6 +330,7 @@ pub(crate) fn lint_stdin(
                 package,
                 settings,
                 noqa,
+                Some(&source_kind),
             );
             let fixed = FxHashMap::default();
 
@@ -333,6 +348,7 @@ pub(crate) fn lint_stdin(
             package,
             settings,
             noqa,
+            Some(&source_kind),
         );
         let fixed = FxHashMap::default();
         (result, fixed)
diff --git a/crates/ruff_dev/src/print_tokens.rs b/crates/ruff_dev/src/print_tokens.rs
index 39b05b3a6236e..d8e62051dfde0 100644
--- a/crates/ruff_dev/src/print_tokens.rs
+++ b/crates/ruff_dev/src/print_tokens.rs
@@ -12,11 +12,19 @@ pub(crate) struct Args {
     /// Python file for which to generate the AST.
     #[arg(required = true)]
     file: PathBuf,
+    /// Run in Jupyter mode i.e., allow line magics (%), shell commands (!), and help (?).
+    #[arg(long)]
+    jupyter: bool,
 }
 
 pub(crate) fn main(args: &Args) -> Result<()> {
     let contents = fs::read_to_string(&args.file)?;
-    for (tok, range) in lexer::lex(&contents, Mode::Module).flatten() {
+    let mode = if args.jupyter {
+        Mode::Jupyter
+    } else {
+        Mode::Module
+    };
+    for (tok, range) in lexer::lex(&contents, mode).flatten() {
         println!(
             "{start:#?} {tok:#?} {end:#?}",
             start = range.start(),
diff --git a/crates/ruff_python_ast/src/token_kind.rs b/crates/ruff_python_ast/src/token_kind.rs
index 7b460eba20a91..a0745aef55597 100644
--- a/crates/ruff_python_ast/src/token_kind.rs
+++ b/crates/ruff_python_ast/src/token_kind.rs
@@ -19,6 +19,8 @@ pub enum TokenKind {
     /// Token value for a newline that is not a logical line break. These are filtered out of
     /// the token stream prior to parsing.
     NonLogicalNewline,
+    /// Token value for a Jupyter magic command.
+    MagicCommand,
     /// Token value for an indent.
     Indent,
     /// Token value for a dedent.
@@ -341,6 +343,7 @@ impl TokenKind {
             Tok::Comment(_) => TokenKind::Comment,
             Tok::Newline => TokenKind::Newline,
             Tok::NonLogicalNewline => TokenKind::NonLogicalNewline,
+            Tok::MagicCommand(_) => TokenKind::MagicCommand,
             Tok::Indent => TokenKind::Indent,
             Tok::Dedent => TokenKind::Dedent,
             Tok::EndOfFile => TokenKind::EndOfFile,
diff --git a/crates/ruff_rustpython/src/lib.rs b/crates/ruff_rustpython/src/lib.rs
index c0fcd72e28081..1203ba82b33b7 100644
--- a/crates/ruff_rustpython/src/lib.rs
+++ b/crates/ruff_rustpython/src/lib.rs
@@ -4,9 +4,9 @@ use rustpython_parser::lexer::LexResult;
 use rustpython_parser::{lexer, Mode, ParseError};
 
 /// Collect tokens up to and including the first error.
-pub fn tokenize(contents: &str) -> Vec<LexResult> {
+pub fn tokenize(contents: &str, mode: Mode) -> Vec<LexResult> {
     let mut tokens: Vec<LexResult> = vec![];
-    for tok in lexer::lex(contents, Mode::Module) {
+    for tok in lexer::lex(contents, mode) {
         let is_err = tok.is_err();
         tokens.push(tok);
         if is_err {
@@ -19,9 +19,10 @@ pub fn tokenize(contents: &str) -> Vec<LexResult> {
 /// Parse a full Python program from its tokens.
 pub fn parse_program_tokens(
     lxr: Vec<LexResult>,
+    mode: Mode,
     source_path: &str,
 ) -> anyhow::Result<Suite, ParseError> {
-    parser::parse_tokens(lxr, Mode::Module, source_path).map(|top| match top {
+    parser::parse_tokens(lxr, mode, source_path).map(|top| match top {
         Mod::Module(ModModule { body, .. }) => body,
         _ => unreachable!(),
     })
diff --git a/crates/ruff_wasm/src/lib.rs b/crates/ruff_wasm/src/lib.rs
index 27e3de73c09d6..2fd7ccdbf7fa2 100644
--- a/crates/ruff_wasm/src/lib.rs
+++ b/crates/ruff_wasm/src/lib.rs
@@ -1,6 +1,7 @@
 use std::path::Path;
 
 use rustpython_parser::lexer::LexResult;
+use rustpython_parser::Mode;
 use serde::{Deserialize, Serialize};
 use wasm_bindgen::prelude::*;
 
@@ -180,7 +181,7 @@ pub fn check(contents: &str, options: JsValue) -> Result<JsValue, JsValue> {
         Settings::from_configuration(configuration, Path::new(".")).map_err(|e| e.to_string())?;
 
     // Tokenize once.
-    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents);
+    let tokens: Vec<LexResult> = ruff_rustpython::tokenize(contents, Mode::Module);
 
     // Map row and column locations to byte slices (lazily).
     let locator = Locator::new(contents);