diff --git a/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch b/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch
new file mode 100644
index 000000000000..539afc4b3b77
--- /dev/null
+++ b/pkgs/applications/science/math/sage/patches/numpy-1.25-deprecation.patch
@@ -0,0 +1,18 @@
+diff --git a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
+index aa153fd4cd..eebbe87aff 100644
+--- a/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
++++ b/src/sage/tests/books/computational-mathematics-with-sagemath/graphique_doctest.py
+@@ -134,11 +134,11 @@ Sage example in ./graphique.tex, line 1120::
+   sage: t = srange(0, 5, 0.1); p = Graphics()
+   sage: for k in srange(0, 10, 0.15):
+   ....:       y = integrate.odeint(f, k, t)
+-  ....:       p += line(zip(t, flatten(y)))
++  ....:       p += line(zip(t, y.flatten()))
+   sage: t = srange(0, -5, -0.1); q = Graphics()
+   sage: for k in srange(0, 10, 0.15):
+   ....:       y = integrate.odeint(f, k, t)
+-  ....:       q += line(zip(t, flatten(y)))
++  ....:       q += line(zip(t, y.flatten()))
+   sage: y = var('y')
+   sage: v = plot_vector_field((1, -cos(x*y)), (x,-5,5), (y,-2,11))
+   sage: g = p + q + v; g.show()
diff --git a/pkgs/applications/science/math/sage/sage-src.nix b/pkgs/applications/science/math/sage/sage-src.nix
index d890a65230cb..dee6e8eb0d4b 100644
--- a/pkgs/applications/science/math/sage/sage-src.nix
+++ b/pkgs/applications/science/math/sage/sage-src.nix
@@ -80,6 +80,23 @@ stdenv.mkDerivation rec {
       sha256 = "sha256-k8Oam+EiRcfXC7qCdLacCx+7vpUAw2K1wsjKcQbeGb4=";
     })
 
+    # https://github.com/sagemath/sage/pull/35826, landed in 10.1.beta5
+    (fetchpatch {
+      name = "numpy-1.25.0-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/ecfe06b8f1fe729b07e885f0de55244467e5c137.diff";
+      sha256 = "sha256-G0xhl+LyNdDYPzRqSHK3fHaepcIzpuwmqRiussraDf0=";
+    })
+
+    # https://github.com/sagemath/sage/pull/35826#issuecomment-1658569891
+    ./patches/numpy-1.25-deprecation.patch
+
+    # https://github.com/sagemath/sage/pull/35842, landed in 10.1.beta5
+    (fetchpatch {
+      name = "scipy-1.11-upgrade.patch";
+      url = "https://github.com/sagemath/sage/commit/90ece168c3c61508baa36659b0027b7dd8b43add.diff";
+      sha256 = "sha256-Y5TmuJcUJR+veb2AuSVODGs+xkVV+pTM8fWTm4q+NDs=";
+    })
+
     # https://github.com/sagemath/sage/pull/35825, landed in 10.1.beta6
     (fetchpatch {
       name = "singular-4.3.2p2-upgrade.patch";