diff --git a/doc/contributing.rst b/doc/contributing.rst
index c5d1748..44aab66 100644
--- a/doc/contributing.rst
+++ b/doc/contributing.rst
@@ -44,7 +44,7 @@ line-length of 119 characters. Documentation, comments, and docstrings should be
 .. _PEP 8: https://www.python.org/dev/peps/pep-0008/
 .. _black: https://pypi.org/project/black/
 
-PyStan code is also checked by ``flake8`` and ``mypy``.
+PyStan code is also checked by ``mypy``.
 
 Commit Messages
 ===============
diff --git a/pyproject.toml b/pyproject.toml
index b3289b1..a504558 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -34,12 +34,10 @@ setuptools = "*"
 pytest = "^6.2"
 pytest-asyncio = "^0.18.3"
 pandas = "^1.0"
-autoflake = "^1.4"
 black = "22.6.0"
 isort = "^5.9"
 mypy = "0.982"
 types-setuptools = "^57.4"
-flake8 = "^4.0"
 # documentation
 # NOTE: when changing these, update docs-requirements.txt
 sphinx = "^7.2"
diff --git a/scripts/check b/scripts/check
index b638fa3..105f3d7 100755
--- a/scripts/check
+++ b/scripts/check
@@ -7,7 +7,6 @@ set -x
 
 isort --check --diff $SOURCE_FILES
 black --check --diff $SOURCE_FILES
-flake8 $SOURCE_FILES
 mypy $SOURCE_FILES
 
 # verify building documentation succeeds
diff --git a/scripts/lint b/scripts/lint
index fb9dab2..bd43373 100755
--- a/scripts/lint
+++ b/scripts/lint
@@ -5,6 +5,5 @@ SOURCE_FILES="stan tests"
 
 set -x
 
-autoflake --in-place --recursive $SOURCE_FILES
 isort $SOURCE_FILES
 black $SOURCE_FILES scripts doc
diff --git a/setup.cfg b/setup.cfg
index 2b2eaae..976ba02 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,8 +1,2 @@
-# flake8 cannot be configured using pyproject.toml
-[flake8]
-max-line-length = 119
-extend-ignore = E203, E501, W503
-exclude = .venv,.git,dist,doc,*lib/python*,*egg,build
-
 [mypy]
 ignore_missing_imports = True