diff --git a/crates/ruff/tests/integration_test.rs b/crates/ruff/tests/integration_test.rs
index 81490045657706..380974918f70e4 100644
--- a/crates/ruff/tests/integration_test.rs
+++ b/crates/ruff/tests/integration_test.rs
@@ -629,6 +629,42 @@ fn stdin_override_parser_py() {
     ");
 }
 
+#[test]
+fn stdin_override_parser_py_config() -> Result<()> {
+    let tempdir = TempDir::new()?;
+    let pyproject_toml = tempdir.path().join("pyproject.toml");
+    fs::write(
+        &pyproject_toml,
+        r#"
+[tool.ruff]
+extension = {ipynb="python"}
+"#,
+    )?;
+    let mut cmd = RuffCheck::default()
+        .config(&pyproject_toml)
+        .args(["--stdin-filename", "F401.ipynb"])
+        .build();
+    assert_cmd_snapshot!(cmd
+        .pass_stdin("import os\n"), @"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    F401 [*] `os` imported but unused
+     --> F401.ipynb:1:8
+      |
+    1 | import os
+      |        ^^
+      |
+    help: Remove unused import: `os`
+
+    Found 1 error.
+    [*] 1 fixable with the `--fix` option.
+
+    ----- stderr -----
+    ");
+    Ok(())
+}
+
 #[test]
 fn stdin_fix_when_not_fixable_should_still_print_contents() {
     let mut cmd = RuffCheck::default().args(["--fix"]).build();
diff --git a/crates/ruff_workspace/src/configuration.rs b/crates/ruff_workspace/src/configuration.rs
index 5c204b3a0078ce..59c9be0efe760e 100644
--- a/crates/ruff_workspace/src/configuration.rs
+++ b/crates/ruff_workspace/src/configuration.rs
@@ -564,10 +564,7 @@ impl Configuration {
                     })
                     .collect()
             }),
-            // `--extension` is a hidden command-line argument that isn't supported in configuration
-            // files at present.
-            extension: None,
-
+            extension: options.extension.map(ExtensionMapping::from),
             lint: LintConfiguration::from_options(lint, project_root)?,
             format: FormatConfiguration::from_options(
                 options.format.unwrap_or_default(),
diff --git a/crates/ruff_workspace/src/options.rs b/crates/ruff_workspace/src/options.rs
index 07011ad66026c4..78e35073a1d043 100644
--- a/crates/ruff_workspace/src/options.rs
+++ b/crates/ruff_workspace/src/options.rs
@@ -32,7 +32,7 @@ use ruff_linter::rules::{
     pycodestyle, pydoclint, pydocstyle, pyflakes, pylint, pyupgrade, ruff,
 };
 use ruff_linter::settings::types::{
-    IdentifierPattern, OutputFormat, PythonVersion, RequiredVersion,
+    IdentifierPattern, Language, OutputFormat, PythonVersion, RequiredVersion,
 };
 use ruff_linter::{RuleSelector, warn_user_once};
 use ruff_macros::{CombineOptions, OptionsMetadata};
@@ -282,6 +282,20 @@ pub struct Options {
     )]
     pub respect_gitignore: Option<bool>,
 
+    /// A mapping of custom file extensions to known file types (overridden
+    /// by the `--extension` command-line flag).
+    ///
+    /// Supported file types include `python`, `pyi`, `ipynb`, and `markdown`.
+    #[option(
+        default = "{}",
+        value_type = "dict[str, Language]",
+        example = r#"
+            # Add a custom file extension mapped to Python
+            extension = {rpy="python"}
+        "#
+    )]
+    pub extension: Option<FxHashMap<String, Language>>,
+
     // Generic python options
     /// A list of builtins to treat as defined references, in addition to the
     /// system builtins.
diff --git a/ruff.schema.json b/ruff.schema.json
index 1de42c71a9ba7e..8d95d780644f4b 100644
--- a/ruff.schema.json
+++ b/ruff.schema.json
@@ -177,6 +177,16 @@
         "$ref": "#/definitions/RuleSelector"
       }
     },
+    "extension": {
+      "description": "A mapping of custom file extensions to known file types (overridden\nby the `--extension` command-line flag).\n\nSupported file types include `python`, `pyi`, `ipynb`, and `markdown`.",
+      "type": [
+        "object",
+        "null"
+      ],
+      "additionalProperties": {
+        "$ref": "#/definitions/Language"
+      }
+    },
     "external": {
       "description": "A list of rule codes or prefixes that are unsupported by Ruff, but should be\npreserved when (e.g.) validating `# noqa` directives. Useful for\nretaining `# noqa` directives that cover plugins not yet implemented\nby Ruff.",
       "type": [
@@ -1976,6 +1986,15 @@
       },
       "additionalProperties": false
     },
+    "Language": {
+      "type": "string",
+      "enum": [
+        "python",
+        "pyi",
+        "ipynb",
+        "markdown"
+      ]
+    },
     "LineEnding": {
       "oneOf": [
         {