diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 01c034e763..df9c1b1bb6 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -82,10 +82,6 @@ jobs:
           path: |
             ./autotest/.failed/**
 
-      - name: Run notebooks
-        working-directory: scripts
-        run: python run_notebooks.py
-
       - name: Generate changelog
         id: cliff
         uses: orhun/git-cliff-action@v3
diff --git a/docs/make_release.md b/docs/make_release.md
index 455af25424..d65c7619f5 100644
--- a/docs/make_release.md
+++ b/docs/make_release.md
@@ -100,8 +100,6 @@ As described above, making a release manually involves the following steps:
 
 - Run `ruff check .` and `ruff format .` from the project root.
 
-- Use `run_notebooks.py` in the `scripts` directory to rerun all notebooks in `.docs/Notebooks`.
-
 - Generate a changelog starting from the last release with [git cliff](https://github.com/orhun/git-cliff), for instance: `git cliff --config cliff.toml --unreleased --tag=<release version number>`.
 
 - Prepend the release changelog to the comprehensive changelog file `docs/version_changes.md`.
diff --git a/scripts/README.md b/scripts/README.md
index 45d5166057..71ed667f2e 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -28,12 +28,6 @@ For instance, `e689af57e7439b9005749d806248897ad550eab5_20150811_041632_uncommit
 
 **Note**: the `process_benchmarks.py` script depends on `seaborn`, which is not included as a dependency in either `etc/environment.yml` or in any of the optional groups in `pyproject.toml`, since this is the only place it is used in this repository.
 
-## Running notebooks
-
-The `run_notebooks.py` script runs notebooks located in the `.docs/Notebooks` directory.
-
-Notebooks are run using `jupytext --from_ipynb --execute <notebook path>`. Note that notebooks are under version control, and running them with this script will produce large changesets in your working tree as outputs and execution metadata are updated. See the [developer docs](../DEVELOPER.md) for instructions to configure `git` to automatically strip notebook outputs before commits.
-
 ## Updating version
 
 The `update_version.py` script can be used to update FloPy version numbers. Running the script first updates the version in `version.txt`, then propagates the change to various other places version strings or timestamps are embedded in the repository:
diff --git a/scripts/run_notebooks.py b/scripts/run_notebooks.py
deleted file mode 100644
index 7569c2259a..0000000000
--- a/scripts/run_notebooks.py
+++ /dev/null
@@ -1,47 +0,0 @@
-import os
-import sys
-
-# path to notebooks
-src_pths = (os.path.join("..", ".docs", "Notebooks"),)
-
-# parse command line arguments for notebook to create
-nb_files = None
-for idx, arg in enumerate(sys.argv):
-    if arg in ("-f", "--file"):
-        file_name = sys.argv[idx + 1]
-        if not file_name.endswith(".ipynb"):
-            file_name += ".ipynb"
-        for src_pth in src_pths:
-            src = os.path.join(src_pth, file_name)
-            if os.path.isfile(src):
-                nb_files = [src]
-                break
-
-# get list of notebooks
-if nb_files is None:
-    nb_files = []
-    for src_pth in src_pths:
-        nb_files += [
-            os.path.join(src_pth, file_name)
-            for file_name in sorted(os.listdir(src_pth))
-            if file_name.endswith(".ipynb")
-        ]
-
-failed_runs = []
-
-# run the notebooks
-for src in nb_files:
-    arg = (
-        "jupytext",
-        "--from ipynb",
-        "--execute",
-        src,
-    )
-    print(" ".join(arg))
-    return_code = os.system(" ".join(arg))
-    if return_code != 0:
-        failed_runs.append(src)
-
-# write out failed runs
-for idx, src in enumerate(failed_runs):
-    print(f"{idx + 1:2d}...{src} FAILED")