--- a/eigen3.pc.in	
+++ a/eigen3.pc.in	
@@ -1,6 +1,9 @@ 
+prefix=${CMAKE_INSTALL_PREFIX}
+exec_prefix=${prefix}
+
 Name: Eigen3
 Description: A C++ template library for linear algebra: vectors, matrices, and related algorithms
 Requires:
 Version: ${EIGEN_VERSION_NUMBER}
 Libs:
-Cflags: -I${INCLUDE_INSTALL_DIR}
+Cflags: -I${prefix}/${INCLUDE_INSTALL_DIR}