OSError: [Errno 39] Directory not empty in Python (tested)

OSError: [Errno 39] Directory not empty (ENOTEMPTY) comes from os.rmdir, Path.rmdir or os.removedirs on a directory that still has contents, and from os.rename onto an existing non-empty directory. Use shutil.rmtree to delete a tree, or copytree(..., dirs_exist_ok=True) to merge.

1. The error

import os
os.makedirs("out/logs", exist_ok=True)
open("out/logs/a.txt", "w").close()
os.rmdir("out/logs")

Output:

Traceback (most recent call last):
  File "/tmp/dn/b1.py", line 4, in <module>
    os.rmdir("out/logs")
    ~~~~~~~~^^^^^^^^^^^^
OSError: [Errno 39] Directory not empty: 'out/logs'

os.rmdir() only removes empty directories. Anything inside (files, subdirectories, hidden files such as .DS_Store) makes it fail with ENOTEMPTY.

2. pathlib.Path.rmdir and os.removedirs behave the same

import os, pathlib
os.makedirs("out2/sub", exist_ok=True)
open("out2/sub/a.txt", "w").close()
for f in (lambda: pathlib.Path("out2/sub").rmdir(), lambda: os.removedirs("out2/sub")):
    try:
        f()
    except OSError as e:
        print(type(e).__name__, e.errno, e)

Output:

OSError 39 [Errno 39] Directory not empty: 'out2/sub'
OSError 39 [Errno 39] Directory not empty: 'out2/sub'

Neither deletes contents. os.removedirs only prunes empty parents after removing an empty leaf.

3. os.rename onto an existing directory

import os
os.makedirs("new/x", exist_ok=True); os.makedirs("old/y", exist_ok=True)
try:
    os.rename("new", "old")          # target dir exists and is not empty
except OSError as e:
    print(type(e).__name__, e)
os.makedirs("empty", exist_ok=True)
os.rename("new", "empty")            # an EMPTY target directory is replaced
print("renamed onto empty dir:", os.listdir("empty"))

Output:

OSError [Errno 39] Directory not empty: 'new' -> 'old'
renamed onto empty dir: ['x']

On Linux, renaming a directory onto an existing non-empty directory raises the same error, while an empty target is silently replaced. This shows up in deploy scripts that do os.rename("build_new", "build") on the second run.

4. Fix: shutil.rmtree, or merge with copytree

import os, shutil
os.makedirs("out3/logs/deep", exist_ok=True)
open("out3/logs/deep/a.txt", "w").close()
shutil.rmtree("out3")
print("exists after rmtree:", os.path.exists("out3"))

os.makedirs("src/x", exist_ok=True); os.makedirs("dst/old", exist_ok=True)
shutil.copytree("src", "dst", dirs_exist_ok=True)   # merge instead of rename
print("dst:", sorted(os.listdir("dst")))

Output:

exists after rmtree: False
dst: ['old', 'x']

shutil.rmtree deletes the whole tree. To merge into an existing directory instead of replacing it, use shutil.copytree(src, dst, dirs_exist_ok=True) (Python 3.8+). To replace atomically-ish, rename the old directory away first, rename the new one in, then rmtree the old one.

5. Catch it precisely

import errno, os
os.makedirs("out4/a", exist_ok=True)
try:
    os.rmdir("out4")
except OSError as e:
    print(errno.errorcode[e.errno], "| ENOTEMPTY == e.errno:", e.errno == errno.ENOTEMPTY)
    print("subclass:", type(e).__name__, "| ls:", os.listdir("out4"))

Output:

ENOTEMPTY | ENOTEMPTY == e.errno: True
subclass: OSError | ls: ['a']

It is a plain OSError (no subclass); check e.errno == errno.ENOTEMPTY.

Related: shutil error handling · rmtree PermissionError · [Errno 16] Device or resource busy.

Written with AI assistance. Measured on 2026-10-23 with Python 3.13.5 on Linux (Debian 13, ext4). Each block was run verbatim and the output pasted unedited. PlainTables is our extension; Python is free.