diff --git a/template/.config/mypy.ini b/template/.config/mypy.ini
deleted file mode 100644
index f6c48ee..0000000
--- a/template/.config/mypy.ini
+++ /dev/null
@@ -1,9 +0,0 @@
-[mypy]
-python_version = 3.12
-strict = True
-
-[mypy-quartodoc.*]
-ignore_missing_imports = True
-
-[mypy-tests.*]
-disallow_untyped_defs = False
diff --git a/template/.pre-commit-config.yaml b/template/.pre-commit-config.yaml
index c5e4590..1d7e890 100644
--- a/template/.pre-commit-config.yaml
+++ b/template/.pre-commit-config.yaml
@@ -32,6 +32,7 @@ repos:
     rev: v1.46.2
     hooks:
       - id: typos
+        args: [--config, .config/typos.toml, --force-exclude]
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
@@ -42,3 +43,13 @@ repos:
         args: [--fix]
       # Run the formatter.
       - id: ruff-format
+
+  - repo: https://github.com/facebook/pyrefly-pre-commit
+    # Note: this is the version of the pre-commit hook, NOT the pyrefly version used for type checking.
+    rev: 1.2.0.dev1
+    hooks:
+      - id: pyrefly-check
+        name: Pyrefly (type checking)
+        # Recommended to do full repo checks, not just on changed files.
+        pass_filenames: false
+        language: system
diff --git a/template/.vscode/extensions.json b/template/.vscode/extensions.json
index 877612b..c830a88 100644
--- a/template/.vscode/extensions.json
+++ b/template/.vscode/extensions.json
@@ -8,7 +8,7 @@
     "GitHub.vscode-pull-request-github",
     "ms-python.python",
     "ms-python.vscode-pylance",
-    "matangover.mypy",
+    "meta.pyrefly",
     "njpwerner.autodocstring",
     "quarto.quarto",
     "ms-toolsai.jupyter",
diff --git a/template/.vscode/settings.json b/template/.vscode/settings.json
index 46d6c2e..41a8a63 100644
--- a/template/.vscode/settings.json
+++ b/template/.vscode/settings.json
@@ -28,8 +28,6 @@
   "files.insertFinalNewline": true,
   "python.testing.pytestEnabled": true,
   "python.testing.pytestPath": "${workspaceFolder}/.venv/bin/pytest",
-  "mypy.runUsingActiveInterpreter": true,
-  "mypy.configFile": ".config/mypy.ini",
   "conventionalCommits.emojiFormat": "emoji",
   "conventionalCommits.promptScopes": false,
   "typos.config": ".config/typos.toml",
diff --git a/template/CONTRIBUTING.md.jinja b/template/CONTRIBUTING.md.jinja
index 31f7211..347a83c 100644
--- a/template/CONTRIBUTING.md.jinja
+++ b/template/CONTRIBUTING.md.jinja
@@ -28,7 +28,7 @@ It's easiest to install uv and justfile using
 install uv and justfile by running:
 
 ``` bash
-pipx install uv rust-just
+pipx install uv rust-just pyrefly
 ```
 
 We keep all our development workflows in the `justfile`, so you can
@@ -79,19 +79,15 @@ commit.
   such as:
     - `quartodoc.py`: Custom
       [`quartodoc`](https://machow.github.io/quartodoc/) renderer.
-    - `mypy.ini`: [`mypy`](https://mypy.readthedocs.io/en/stable/)
-      configuration file for type checking Python code.
     - `ruff.toml`: [Ruff](https://docs.astral.sh/ruff/) configuration file
       for linting and formatting Python code.
     - `rumdl.toml` and `panache.toml`: [rumdl](https://rumdl.dev) and
       [Panache](https://panache.bz) configuration file for formatting Markdown
       files in the project.
-    {% if for_seedcase -%}
     - `cog.toml`: [Cocogitto](https://docs.cocogitto.io) configuration file
       for managing versions.
     - `cliff.toml`: [git-cliff](https://git-cliff.org) configuration file for
       creating the changelog.
-    {%- endif %}
 - `.copier-answers.yml`: Contains the answers you gave when copying the
   package from the template.
   **You should not modify this file directly.**
diff --git a/template/TODO.md b/template/TODO.md
index c74d04d..8af94e6 100644
--- a/template/TODO.md
+++ b/template/TODO.md
@@ -4,7 +4,7 @@
   project.
 - Run `git init -b main` to create the project as a Git repository.
 - Install these packages
-  `uv add --dev pytest genbadge jupyter pytest-cov quartodoc quarto types-tabulate mypy`
+  `uv add --dev pytest genbadge jupyter pytest-cov quartodoc quarto types-tabulate`
 - Run `just list-todos` and complete all the TODO items.
 - Run `just install-precommit` to install the pre-commit hooks.
 - Run `just build-readme` to build the Markdown version of the README. {%- if
diff --git a/template/justfile.jinja b/template/justfile.jinja
index 795f310..a9c661e 100644
--- a/template/justfile.jinja
+++ b/template/justfile.jinja
@@ -72,7 +72,7 @@ check-python:
   # Check formatting
   uvx ruff check .
   # Check types
-  uv run mypy --pretty . --config-file .config/mypy.ini
+  uvx pyrefly check
 
 # Run basic security checks on the package
 check-security:
diff --git a/template/pyproject.toml.jinja b/template/pyproject.toml.jinja
index d5b41a0..3ef8e0f 100644
--- a/template/pyproject.toml.jinja
+++ b/template/pyproject.toml.jinja
@@ -20,7 +20,7 @@ dependencies = []
 classifiers = [
   "License :: OSI Approved :: MIT License",
 
-  # Strict typing, checked via mypy
+  # Strict typing, checked via Pyrefly
   "Typing :: Typed",
 
   # How mature is this project? Common values are
@@ -57,5 +57,11 @@ build-backend = "hatchling.build"
 # - Trigger failure if below 90% code coverage
 addopts = "--tb=short --import-mode=importlib --cov=src --no-cov-on-fail --cov-report=term --cov-report=xml --cov-report=html --cov-fail-under=90"
 
+[tool.pyrefly]
+project-includes = ["src/"]
+min-severity = "warn"
+python-version = "3.12.0"
+preset = "strict"
+
 [tool.ruff]
 extend = ".config/ruff.toml"
diff --git a/template/tools/vulture-allowlist.py b/template/tools/vulture-allowlist.py
index 44a7814..d65b8af 100644
--- a/template/tools/vulture-allowlist.py
+++ b/template/tools/vulture-allowlist.py
@@ -1,2 +1 @@
 # ruff: noqa
-# mypy: ignore-errors