diff --git a/api/db/migrations/20241126150201_update-constraint-national-student-id-organization-id-deleted-at.js b/api/db/migrations/20241126150201_update-constraint-national-student-id-organization-id-deleted-at.js
new file mode 100644
index 00000000000..ad2109248f2
--- /dev/null
+++ b/api/db/migrations/20241126150201_update-constraint-national-student-id-organization-id-deleted-at.js
@@ -0,0 +1,32 @@
+const TABLE_NAME = 'organization-learners';
+const NEW_CONSTRAINT_NAME = 'one_active_sco_organization_learner';
+const DELETEDAT_COLUMN = 'deletedAt';
+const NATIONAL_STUDENT_ID_COLUMN = 'nationalStudentId';
+const ORGANIZATIONID_COLUMN = 'organizationId';
+
+const up = async function (knex) {
+  await knex.schema.table(TABLE_NAME, (table) => {
+    table.dropUnique(['organizationId', 'nationalStudentId']);
+  });
+
+  return knex.raw(
+    `CREATE UNIQUE INDEX :name: ON :table: (:nationalStudentId:, :organizationId: ) WHERE :deletedAt: IS NULL;`,
+    {
+      name: NEW_CONSTRAINT_NAME,
+      table: TABLE_NAME,
+      nationalStudentId: NATIONAL_STUDENT_ID_COLUMN,
+      organizationId: ORGANIZATIONID_COLUMN,
+      deletedAt: DELETEDAT_COLUMN,
+    },
+  );
+};
+
+const down = async function (knex) {
+  await knex.raw(`DROP INDEX :name:;`, { name: NEW_CONSTRAINT_NAME });
+
+  return knex.schema.table(TABLE_NAME, (table) => {
+    table.unique(['organizationId', 'nationalStudentId']);
+  });
+};
+
+export { down, up };
diff --git a/api/src/prescription/learner-management/infrastructure/repositories/organization-learner-repository.js b/api/src/prescription/learner-management/infrastructure/repositories/organization-learner-repository.js
index 42c63a26384..54dbdc45083 100644
--- a/api/src/prescription/learner-management/infrastructure/repositories/organization-learner-repository.js
+++ b/api/src/prescription/learner-management/infrastructure/repositories/organization-learner-repository.js
@@ -97,7 +97,7 @@ const addOrUpdateOrganizationOfOrganizationLearners = async function (organizati
 
     await knexConn('organization-learners')
       .insert(organizationLearnersToSave)
-      .onConflict(['organizationId', 'nationalStudentId'])
+      .onConflict(knexConn.raw('("organizationId","nationalStudentId") where "deletedAt" is NULL'))
       .merge();
   } catch (err) {
     throw new OrganizationLearnersCouldNotBeSavedError();
diff --git a/api/tests/prescription/learner-management/integration/infrastructure/repositories/organization-learner-repository_test.js b/api/tests/prescription/learner-management/integration/infrastructure/repositories/organization-learner-repository_test.js
index c8456b3ed0d..6ff0d1f0ff1 100644
--- a/api/tests/prescription/learner-management/integration/infrastructure/repositories/organization-learner-repository_test.js
+++ b/api/tests/prescription/learner-management/integration/infrastructure/repositories/organization-learner-repository_test.js
@@ -580,6 +580,56 @@ describe('Integration | Repository | Organization Learner Management | Organizat
       });
     });
 
+    context('when there are deleted organizationLearners with same nationalStudentId', function () {
+      let organizationLearners;
+      let organizationId;
+      let firstOrganizationLearner;
+
+      beforeEach(async function () {
+        organizationId = databaseBuilder.factory.buildOrganization().id;
+
+        firstOrganizationLearner = new OrganizationLearner({
+          lastName: 'Pipeau',
+          preferredLastName: 'Toto',
+          firstName: 'Corinne',
+          middleName: 'Dorothée',
+          thirdName: 'Driss',
+          sex: 'F',
+          birthdate: '2000-01-01',
+          birthCity: 'Perpi',
+          birthCityCode: '123456',
+          birthProvinceCode: '66',
+          birthCountryCode: '100',
+          MEFCode: 'MEF123456',
+          status: 'ST',
+          nationalStudentId: '1234',
+          division: '4B',
+          userId: null,
+          isDisabled: false,
+          organizationId,
+        });
+
+        databaseBuilder.factory.buildOrganizationLearner({ ...firstOrganizationLearner, deletedAt: new Date() });
+
+        await databaseBuilder.commit();
+
+        organizationLearners = [firstOrganizationLearner];
+      });
+
+      it('should create all organizationLearners', async function () {
+        // when
+        await DomainTransaction.execute((domainTransaction) => {
+          return addOrUpdateOrganizationOfOrganizationLearners(organizationLearners, organizationId, domainTransaction);
+        });
+
+        // then
+        const actualOrganizationLearners = await organizationLearnerRepository.findByOrganizationId({
+          organizationId,
+        });
+        expect(actualOrganizationLearners).to.have.lengthOf(1);
+      });
+    });
+
     context('when an organizationLearner is saved with a userId already present in organization', function () {
       it('should save the organization learner with userId as null', async function () {
         const { id: organizationId } = databaseBuilder.factory.buildOrganization();