diff --git a/Configurations.md b/Configurations.md
index 2d01fb3bb3b..70abb009e9e 100644
--- a/Configurations.md
+++ b/Configurations.md
@@ -1306,6 +1306,26 @@ If you want to ignore every file under the directory where you put your rustfmt.
 ignore = ["/"]
 ```
 
+## `report_missing_submod`
+
+Controls whether to report missing submodules and whether rustfmt will format.
+
+- **Default value**: `Error`
+- **Possible values**: `Error`, `Warn`, `Ignore`
+- **Stable**: No
+
+#### `Error` (default):
+
+Missing modules will lead to module not found errors and rustfmt won't format anything.
+
+#### `Warn`
+
+Missing modules will lead to module not found warnings and rustfmt will format.
+
+#### `Ignore`
+
+Ignores missing submodule error and rustfmt will format.
+
 ## `imports_indent`
 
 Indent style of imports
diff --git a/src/config/mod.rs b/src/config/mod.rs
index 9484b2e5829..772b09dd8c4 100644
--- a/src/config/mod.rs
+++ b/src/config/mod.rs
@@ -179,6 +179,8 @@ create_config! {
          or they are left with trailing whitespaces";
     ignore: IgnoreList, IgnoreList::default(), false,
         "Skip formatting the specified files and directories";
+    report_missing_submod: ReportMissingSubmod, ReportMissingSubmod::Error, false,
+        "Report missing submodule";
 
     // Not user-facing
     verbose: Verbosity, Verbosity::Normal, false, "How much to information to emit to the user";
@@ -697,6 +699,7 @@ show_parse_errors = true
 error_on_line_overflow = false
 error_on_unformatted = false
 ignore = []
+report_missing_submod = "Error"
 emit_mode = "Files"
 make_backup = false
 "#,
diff --git a/src/config/options.rs b/src/config/options.rs
index 3c5c713a33a..e9edc607f0b 100644
--- a/src/config/options.rs
+++ b/src/config/options.rs
@@ -494,3 +494,14 @@ pub enum StyleEdition {
     /// [Edition 2024]().
     Edition2024,
 }
+
+/// Controls whether to report missing submodules and whether rustfmt will format.
+#[config_type]
+pub enum ReportMissingSubmod {
+    /// Missing modules will lead to module not found errors and rustfmt won't format anything.
+    Error,
+    /// Missing modules will lead to module not found warnings and rustfmt will format.
+    Warn,
+    /// Ignores missing submodule error and rustfmt will format.
+    Ignore,
+}
diff --git a/src/formatting.rs b/src/formatting.rs
index 60361505a3f..f24233c91d7 100644
--- a/src/formatting.rs
+++ b/src/formatting.rs
@@ -135,6 +135,7 @@ fn format_project<T: FormatHandler>(
         &context.parse_session,
         directory_ownership.unwrap_or(DirectoryOwnership::UnownedViaBlock),
         !input_is_stdin && !config.skip_children(),
+        config.report_missing_submod(),
     )
     .visit_crate(&krate)?
     .into_iter()
diff --git a/src/modules.rs b/src/modules.rs
index af9a154a6ae..38f993fbcfa 100644
--- a/src/modules.rs
+++ b/src/modules.rs
@@ -10,7 +10,7 @@ use thin_vec::ThinVec;
 use thiserror::Error;
 
 use crate::attr::MetaVisitor;
-use crate::config::FileName;
+use crate::config::{FileName, ReportMissingSubmod};
 use crate::items::is_mod_decl;
 use crate::parse::parser::{
     Directory, DirectoryOwnership, ModError, ModulePathSuccess, Parser, ParserError,
@@ -62,6 +62,7 @@ pub(crate) struct ModResolver<'ast, 'sess> {
     directory: Directory,
     file_map: FileModMap<'ast>,
     recursive: bool,
+    report_missing_submod: ReportMissingSubmod,
 }
 
 /// Represents errors while trying to resolve modules.
@@ -105,6 +106,7 @@ impl<'ast, 'sess, 'c> ModResolver<'ast, 'sess> {
         parse_sess: &'sess ParseSess,
         directory_ownership: DirectoryOwnership,
         recursive: bool,
+        report_missing_submod: ReportMissingSubmod,
     ) -> Self {
         ModResolver {
             directory: Directory {
@@ -114,6 +116,7 @@ impl<'ast, 'sess, 'c> ModResolver<'ast, 'sess> {
             file_map: BTreeMap::new(),
             parse_sess,
             recursive,
+            report_missing_submod,
         }
     }
 
@@ -249,6 +252,20 @@ impl<'ast, 'sess, 'c> ModResolver<'ast, 'sess> {
             // mod foo;
             // Look for an extern file.
             self.find_external_module(item.ident, &item.attrs, sub_mod)
+                .or_else(|err| match err.kind {
+                    ModuleResolutionErrorKind::NotFound { file: _ }
+                        if self.report_missing_submod == ReportMissingSubmod::Ignore =>
+                    {
+                        Ok(None)
+                    }
+                    ModuleResolutionErrorKind::NotFound { file: _ }
+                        if self.report_missing_submod == ReportMissingSubmod::Warn =>
+                    {
+                        eprintln!("Warning: {}", err);
+                        Ok(None)
+                    }
+                    _ => Err(err),
+                })
         } else {
             // An internal module (`mod foo { /* ... */ }`);
             Ok(Some(SubModKind::Internal(item)))
diff --git a/tests/rustfmt/main.rs b/tests/rustfmt/main.rs
index 87b55ca1d1d..74eae3e9c08 100644
--- a/tests/rustfmt/main.rs
+++ b/tests/rustfmt/main.rs
@@ -1,8 +1,8 @@
 //! Integration tests for rustfmt.
 
 use std::env;
-use std::fs::remove_file;
-use std::path::Path;
+use std::fs::{read_to_string, remove_file};
+use std::path::{Path, PathBuf};
 use std::process::Command;
 
 use rustfmt_config_proc_macro::rustfmt_only_ci_test;
@@ -200,3 +200,47 @@ fn rustfmt_emits_error_when_control_brace_style_is_always_next_line() {
     let (_stdout, stderr) = rustfmt(&args);
     assert!(!stderr.contains("error[internal]: left behind trailing whitespace"))
 }
+
+#[test]
+fn report_missing_sub_mod_error() {
+    // Ensure that missing submodules cause module not found errors when trying to
+    // resolve submodules with `skip_children=false` and `report_missing_submod=Error`
+    let args = [
+        "--config=skip_children=false,report_missing_submod=Error",
+        "tests/source/issue-5609.rs",
+    ];
+    let (_stdout, stderr) = rustfmt(&args);
+    // Module resolution fails because we're unable to find `missing_submod.rs`
+    assert!(stderr.contains("missing_submod.rs does not exist"))
+}
+
+#[test]
+fn report_missing_sub_mod_warn() {
+    // Ensure that missing submodules cause module not found warnings when trying to
+    // resolve submodules with `skip_children=false` and `report_missing_submod=Warn`
+    let args = [
+        "--emit=stdout",
+        "--config=skip_children=false,report_missing_submod=Warn",
+        "tests/source/issue-5609.rs",
+    ];
+    let (stdout, stderr) = rustfmt(&args);
+    // Module resolution succeed but we emit warnings because we're unable to find `missing_submod.rs`
+    assert!(stderr.contains("missing_submod.rs does not exist"));
+
+    let target = read_to_string(PathBuf::from("tests/target/issue-5609.rs")).unwrap();
+    assert!(stdout.ends_with(&target));
+}
+
+#[test]
+fn ignore_missing_sub_mod_true() {
+    // Ensure that missing submodules don't cause module not found errors when trying to
+    // resolve submodules with `skip_children=false` and `report_missing_submod=Ignore`.
+    let args = [
+        "--emit=stdout",
+        "--config=skip_children=false,report_missing_submod=Ignore",
+        "tests/source/issue-5609.rs",
+    ];
+    let (stdout, _stderr) = rustfmt(&args);
+    let target = read_to_string(PathBuf::from("tests/target/issue-5609.rs")).unwrap();
+    assert!(stdout.ends_with(&target));
+}
diff --git a/tests/source/issue-5609-2.rs b/tests/source/issue-5609-2.rs
new file mode 100644
index 00000000000..413c0829f4d
--- /dev/null
+++ b/tests/source/issue-5609-2.rs
@@ -0,0 +1,8 @@
+// rustfmt-report_missing_submod: Warn
+// rustfmt-skip_children: false
+
+mod missing_submod;
+
+fn test() {
+
+}
diff --git a/tests/source/issue-5609.rs b/tests/source/issue-5609.rs
new file mode 100644
index 00000000000..d7112a4d262
--- /dev/null
+++ b/tests/source/issue-5609.rs
@@ -0,0 +1,8 @@
+// rustfmt-report_missing_submod: Ignore
+// rustfmt-skip_children: false
+
+mod missing_submod;
+
+fn test() {
+
+}
diff --git a/tests/target/issue-5609-2.rs b/tests/target/issue-5609-2.rs
new file mode 100644
index 00000000000..f7b454216bf
--- /dev/null
+++ b/tests/target/issue-5609-2.rs
@@ -0,0 +1,6 @@
+// rustfmt-report_missing_submod: Warn
+// rustfmt-skip_children: false
+
+mod missing_submod;
+
+fn test() {}
diff --git a/tests/target/issue-5609.rs b/tests/target/issue-5609.rs
new file mode 100644
index 00000000000..184cc0aed60
--- /dev/null
+++ b/tests/target/issue-5609.rs
@@ -0,0 +1,6 @@
+// rustfmt-report_missing_submod: Ignore
+// rustfmt-skip_children: false
+
+mod missing_submod;
+
+fn test() {}