diff --git a/runtime/doc/autocmd.txt b/runtime/doc/autocmd.txt
index 0eff0ae69f..9d018012f0 100644
--- a/runtime/doc/autocmd.txt
+++ b/runtime/doc/autocmd.txt
@@ -779,7 +779,7 @@ FileChangedShell		When Vim notices that the modification time of
 				change or when the size of the file changes.
 				|timestamp|
 				Triggered for each changed file, after:
-				- executing a shell command
+				- executing a shell command or |:terminal| job
 				- |:checktime|
 				- |FocusGained|
 
@@ -1169,8 +1169,9 @@ SessionWritePost		After writing a session file by calling
 ShellCmdPost			After executing a shell command with |:!cmd|,
 				|:make| and |:grep|.  Can be used to check for
 				any changed files.
+
 				For non-blocking shell commands, see
-				|job-control|.
+				|TermClose| |job-control|.
 
 							*ShellFilterPost*
 ShellFilterPost			After executing a shell command with
diff --git a/runtime/doc/editing.txt b/runtime/doc/editing.txt
index 128913a7f0..23202e63d8 100644
--- a/runtime/doc/editing.txt
+++ b/runtime/doc/editing.txt
@@ -1543,11 +1543,10 @@ Vim remembers the modification timestamp, mode and size of a file when you
 begin editing it.  This is used to avoid that you have two different versions
 of the same file (without you knowing this).
 
-After a shell command is run (|:!cmd| |suspend| |:read!| |K|) timestamps,
-file modes and file sizes are compared for all buffers in a window.   Vim will
-run any associated |FileChangedShell| autocommands or display a warning for
-any files that have changed.  In the GUI this happens when Vim regains input
-focus.
+After a shell command (|:!cmd| |suspend| |:read!| |K|) or |:terminal| job
+exits: timestamps, file modes and file sizes are compared for all buffers
+in a window.  Nvim will run |FileChangedShell| autocommands or display
+a warning for any files that changed.
 
 							*E321* *E462*
 If you want to automatically reload a file when it has been changed outside of
diff --git a/src/nvim/terminal.c b/src/nvim/terminal.c
index fee844a545..3724bde076 100644
--- a/src/nvim/terminal.c
+++ b/src/nvim/terminal.c
@@ -729,6 +729,11 @@ void terminal_close(Terminal **termpp, int status)
     return;
   }
 
+  if (status >= 0) {  // The job may have changed files on disk, like `do_shell` (":!cmd").
+    did_check_timestamps = false;
+    need_check_timestamps = true;
+  }
+
   if (buf && !is_autocmd_blocked()) {
     save_v_event_T save_v_event;
     dict_T *dict = get_v_event(&save_v_event);
diff --git a/test/functional/terminal/buffer_spec.lua b/test/functional/terminal/buffer_spec.lua
index 65011e0acb..a27ac8cff4 100644
--- a/test/functional/terminal/buffer_spec.lua
+++ b/test/functional/terminal/buffer_spec.lua
@@ -639,6 +639,23 @@ end)
 describe(':terminal buffer', function()
   before_each(clear)
 
+  it('exit emits FileChangedShell #41759', function()
+    local path = t.tmpname()
+    write_file(path, 'foo\n')
+    command('edit ' .. path)
+    command('set noautoread') -- Disable 'autoread' to exercise :checktime specifically.
+    api.nvim_buf_set_lines(0, 0, -1, true, { 'local change' })
+    n.exec('let g:fcs = 0 | autocmd FileChangedShell * let g:fcs = 1')
+    write_file(path, 'external change\n')
+
+    -- Terminal in another tab, so returning to the buffer is not what triggers the check.
+    command('tabnew')
+    fn.jobstart({ testprg('shell-test'), 'EXIT', '0' }, { term = true })
+    retry(nil, 10000, function()
+      eq(1, api.nvim_get_var('fcs'))
+    end)
+  end)
+
   it('can resume suspended PTY process running in fish', function()
     skip(is_os('win'), 'N/A for Windows')
     skip(fn.executable('fish') == 0, 'missing "fish" command')