diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
new file mode 100644
index 0000000..c5811f9
--- /dev/null
+++ b/.github/workflows/docs.yml
@@ -0,0 +1,70 @@
+name: Deploy Sphinx docs to GitHub Pages
+
+on:
+  push:
+    branches: [ main, master, docs/pydata ]
+  pull_request:
+    types: [opened, synchronize, reopened]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+  pull-requests: write
+
+concurrency:
+  group: pages-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -e .[dev]
+
+      - name: Build Sphinx site
+        run: sphinx-build -b html docs docs/_site
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+
+      - name: Comment PR with preview URL
+        if: github.event_name == 'pull_request'
+        uses: actions/github-script@v7
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          script: |
+            const previewUrl = `${{ toJSON(steps.deployment.outputs.page_url) }}`;
+            const issue_number = context.payload.pull_request.number;
+            await github.rest.issues.createComment({
+              owner: context.repo.owner,
+              repo: context.repo.repo,
+              issue_number,
+              body: `🔍 Documentation preview for this PR: ${previewUrl}`
+            });
+
diff --git a/.github/workflows/mkdocs.yaml b/.github/workflows/mkdocs.yaml
index a47e2a4..c2a8428 100644
--- a/.github/workflows/mkdocs.yaml
+++ b/.github/workflows/mkdocs.yaml
@@ -1,11 +1,7 @@
 name: MkDocs Documentation
 
 on:
-  pull_request:
-    types: [opened, synchronize, reopened]
-  push:
-    branches:
-      - master
+  workflow_dispatch:
 
 jobs:
   deploy-preview:
diff --git a/docs/api_reference/datasets/index.md b/docs/api_reference/datasets/index.md
index e69de29..3341a4d 100644
--- a/docs/api_reference/datasets/index.md
+++ b/docs/api_reference/datasets/index.md
@@ -0,0 +1,8 @@
+```{toctree}
+:maxdepth: 1
+
+dataset_base_classes
+graph_serialization
+networkx_view
+```
+
diff --git a/docs/api_reference/index.md b/docs/api_reference/index.md
index b804bae..8a7c041 100644
--- a/docs/api_reference/index.md
+++ b/docs/api_reference/index.md
@@ -2,8 +2,13 @@
 
 This section provides detailed documentation for all public APIs in the polygraph package.
 
-## Main Modules
+```{toctree}
+:maxdepth: 2
 
-- **[Metrics](metrics/index.md)** - MMD metrics and evaluation functions for graph analysis
-- **[Datasets](datasets.md)** - Dataset abstractions and graph storage utilities
-- **[Utils](utils/index.md)** - Utility functions including graph descriptors, kernels, and MMD utilities
+datasets/index
+metrics/mmd
+metrics/frechet
+metrics/polygraphscore
+metrics/interface
+utils/index
+```
diff --git a/docs/api_reference/utils/index.md b/docs/api_reference/utils/index.md
index e69de29..72938e9 100644
--- a/docs/api_reference/utils/index.md
+++ b/docs/api_reference/utils/index.md
@@ -0,0 +1,7 @@
+```{toctree}
+:maxdepth: 1
+
+graph_descriptors
+graph_kernels
+```
+
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..675f064
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,48 @@
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath(".."))
+
+
+project = "PolyGraph"
+copyright = "2025, PolyGraph"
+author = "PolyGraph contributors"
+
+extensions = [
+    "myst_parser",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.mathjax",
+    "sphinx_copybutton",
+]
+
+autosummary_generate = True
+autodoc_typehints = "description"
+
+templates_path = ["_templates"]
+exclude_patterns = [
+    "_build",
+    "Thumbs.db",
+    ".DS_Store",
+]
+
+myst_enable_extensions = [
+    "dollarmath",
+    "amsmath",
+]
+myst_heading_anchors = 3
+
+source_suffix = {
+    ".rst": "restructuredtext",
+    ".md": "markdown",
+}
+
+html_theme = "pydata_sphinx_theme"
+
+html_theme_options = {
+    "show_prev_next": False,
+}
+
+html_static_path = ["_static"]
+
diff --git a/docs/datasets/index.md b/docs/datasets/index.md
index ffb4958..80f1030 100644
--- a/docs/datasets/index.md
+++ b/docs/datasets/index.md
@@ -2,6 +2,10 @@
 
 We provide a variety of benchmark datasets:
 
-- [Synthetic Datasets](small_synthetic.md) - Small datasets of synthetic graphs
-- [Procedural Datasets](procedural.md) - Similar to the synthetic graphs above, but procedurally generated. Datasets may be chosen to be larger.
-- [Real-World Datasets](real_world_topologies.md) - Graphs found in the real world
+```{toctree}
+:maxdepth: 2
+
+small_synthetic
+procedural
+real_world_topologies
+```
diff --git a/docs/index.md b/docs/index.md
index 5192a32..71acabd 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -32,3 +32,20 @@ We provide a few basic tutorials:
 - [Basic Usage](tutorials/basic_usage.md) - How to load datasets and compute metrics
 - [Metrics Overview](tutorials/metrics_overview.md) - An overview of which metrics are implemented in `polygraph` (MMD, PGS, VUN, Frechet Distance)
 - [Custom Datasets](tutorials/custom_datasets.md) - How to build custom datasets and share them
+
+```{toctree}
+:maxdepth: 2
+:caption: Contents
+
+installation
+tutorials/basic_usage
+tutorials/metrics_overview
+tutorials/custom_datasets
+datasets/index
+metrics/gaussian_tv_mmd
+metrics/pgs5
+metrics/rbf_mmd
+metrics/vun
+utils/index
+api_reference/index
+```
diff --git a/docs/utils/index.md b/docs/utils/index.md
new file mode 100644
index 0000000..5381cec
--- /dev/null
+++ b/docs/utils/index.md
@@ -0,0 +1,10 @@
+# Utilities
+
+```{toctree}
+:maxdepth: 1
+
+descriptors
+kernels
+mmd_utils
+```
+
diff --git a/mkdocs.yml b/mkdocs.yml
deleted file mode 100644
index 811b8df..0000000
--- a/mkdocs.yml
+++ /dev/null
@@ -1,60 +0,0 @@
-site_name: polygraph
-theme:
-  name: readthedocs  # Optional, but makes docs look better
-  features:
-    - navigation.expand  # Expands all sections by default
-    - navigation.side.indexes
-
-nav:
-  - index.md
-  - Installation: installation.md
-  - Tutorials:
-    - Basic Usage: tutorials/basic_usage.md
-    - Metrics Overview: tutorials/metrics_overview.md
-    - Custom Datasets: tutorials/custom_datasets.md
-  - Base API Reference:
-    - polygraph.metrics:
-      - Interface: api_reference/metrics/interface.md
-      - MMD: api_reference/metrics/mmd.md
-      - PolyGraphScore: api_reference/metrics/polygraphscore.md
-      - Frechet: api_reference/metrics/frechet.md
-    - polygraph.datasets:
-      - Dataset Base Classes: api_reference/datasets/dataset_base_classes.md
-      - NetworkX View: api_reference/datasets/networkx_view.md
-      - Graph Serialization: api_reference/datasets/graph_serialization.md
-    - polygraph.utils:
-      - Graph Descriptors: api_reference/utils/graph_descriptors.md
-      - Graph Kernels: api_reference/utils/graph_kernels.md
-  - Standardized Metrics:
-    - PGS5: metrics/pgs5.md
-    - Gaussian TV MMD: metrics/gaussian_tv_mmd.md
-    - RBF MMD: metrics/rbf_mmd.md
-    - VUN: metrics/vun.md
-  - Datasets:
-    - Small Synthetic Datasets: datasets/small_synthetic.md
-    - Procedural Datasets: datasets/procedural.md
-    - Real-World Datasets: datasets/real_world_topologies.md
-  - Utils:
-    - Graph Descriptors: utils/descriptors.md
-    - Graph Kernels: utils/kernels.md
-    - MMD Utilities: utils/mmd_utils.md
-
-plugins:
-  - search
-  - mkdocstrings:
-      handlers:
-        python:
-          options:
-            extensions:
-              - scripts/griffe_extension.py:JinjaDocstringExtension
-      paths: [polygraph]
-
-markdown_extensions:
-  - admonition
-  - pymdownx.arithmatex:
-      generic: true
-
-
-extra_javascript:
-  - javascript/mathjax.js
-  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js
diff --git a/pixi.toml b/pixi.toml
index 77a249e..8b843b6 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -12,4 +12,6 @@ polygraph = { path = ".", editable = true, extras = ["dev"] }
 
 [tasks]
 test = "pytest -n auto -sv --skip-slow ./tests"
-docs = "mkdocs build"
\ No newline at end of file
+docs = "sphinx-build -b html docs docs/_build/html"
+docs-sphinx = "sphinx-build -b html docs docs/_build/html"
+docs-serve = "sphinx-autobuild --watch polygraph --watch docs -b html docs docs/_build/html --open-browser --port 8000"
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 73987b4..8364576 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,16 +46,18 @@ dev = [
     "ipykernel",
     "grakel",
     "pytest-profiling",
-    "mkdocs",
-    "mkdocstrings",
-    "mkdocs-material",
-    "mkdocstrings-python",
-    "mkdocs-terminal",
     "tabulate",
     "jinja2",
     "seaborn",
     "tueplots",
-    "typer"
+    "typer",
+    "sphinx",
+    "myst-parser",
+    "pydata-sphinx-theme",
+    "sphinx-copybutton",
+    "sphinx-design",
+    "sphinx-autodoc-typehints",
+    "sphinx-autobuild"
 ]
 gpu = [
     "dgl @ https://data.dgl.ai/wheels/torch-2.4/cu124/dgl-2.4.0%2Bcu124-cp311-cp311-manylinux1_x86_64.whl",
diff --git a/requirements-docs.txt b/requirements-docs.txt
index 910559d..76dd25e 100644
--- a/requirements-docs.txt
+++ b/requirements-docs.txt
@@ -1,5 +1,6 @@
-mkdocs
-mkdocs-material
-mkdocstrings
-mkdocstrings-python
-mkdocs-terminal
+sphinx
+pydata-sphinx-theme
+myst-parser
+sphinx-copybutton
+sphinx-design
+sphinx-autodoc-typehints