diff --git a/pkgs/development/libraries/eigen/default.nix b/pkgs/development/libraries/eigen/default.nix
index a16cb628008b..371805804210 100644
--- a/pkgs/development/libraries/eigen/default.nix
+++ b/pkgs/development/libraries/eigen/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "eigen";
-  version = "3.3.7";
+  version = "3.3.9";
 
   src = fetchFromGitLab {
     owner = "libeigen";
     repo = pname;
     rev = version;
-    hash = "sha256-oXJ4V5rakL9EPtQF0Geptl0HMR8700FdSrOB09DbbMQ=";
+    sha256 = "sha256-JMIG7CLMndUsECfbKpXE3BtVFuAjn+CZvf8GXZpLkFQ=";
   };
 
   patches = [
diff --git a/pkgs/development/libraries/eigen/include-dir.patch b/pkgs/development/libraries/eigen/include-dir.patch
index 7f3bd88557ec..42f8e189c0b7 100644
--- a/pkgs/development/libraries/eigen/include-dir.patch
+++ b/pkgs/development/libraries/eigen/include-dir.patch
@@ -8,7 +8,16 @@
  
  # guard against in-source builds
  
-@@ -408,13 +408,6 @@ install(FILES
+@@ -407,7 +407,7 @@ set(PKGCONFIG_INSTALL_DIR
+     CACHE STRING "The directory relative to CMAKE_PREFIX_PATH where eigen3.pc is installed"
+     )
+ 
+-foreach(var INCLUDE_INSTALL_DIR CMAKEPACKAGE_INSTALL_DIR PKGCONFIG_INSTALL_DIR)
++foreach(var CMAKEPACKAGE_INSTALL_DIR PKGCONFIG_INSTALL_DIR)
+   if(IS_ABSOLUTE "${${var}}")
+     message(FATAL_ERROR "${var} must be relative to CMAKE_PREFIX_PATH. Got: ${${var}}")
+   endif()
+@@ -429,13 +429,6 @@ install(FILES
    DESTINATION ${INCLUDE_INSTALL_DIR} COMPONENT Devel
    )
  
@@ -22,7 +31,7 @@
  add_subdirectory(Eigen)
  
  add_subdirectory(doc EXCLUDE_FROM_ALL)
-@@ -510,8 +503,15 @@ set ( EIGEN_VERSION_MAJOR  ${EIGEN_WORLD_VERSION} )
+@@ -531,8 +524,15 @@ set ( EIGEN_VERSION_MAJOR  ${EIGEN_WORLD_VERSION} )
  set ( EIGEN_VERSION_MINOR  ${EIGEN_MAJOR_VERSION} )
  set ( EIGEN_VERSION_PATCH  ${EIGEN_MINOR_VERSION} )
  set ( EIGEN_DEFINITIONS "")