First, make sure you have the a suitable version installed.
$ pkg-config --cflags gtk+-3.0 -pthread -I/usr/include/gtk-3.0 -I/usr/include/pango-1.0 -I/usr/include/gio-unix-2.0/ -I/usr/include/atk-1.0 -I/usr/include/cairo -I/usr/include/gdk-pixbuf-2.0 -I/usr/include/freetype2 -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1 -I/usr/include/libpng12
pkg-config will output the necessary include parameters so the build script knows where to find the script. If pkg-config returns nothing, make sure you have a gtk development package installed.
Once that is properly set up, add this to the build file's cflags. Find the line in the Makefile that defines the cflags. Add the `pkg-config` in backticks, so when make runs, it will evaluate the flags and include the correct directions.
CFLAGS.target ?= $(CFLAGS)becomes
CFLAGS.target ?= $(CFLAGS) `pkg-config --cflags gtk+-3.0`
If everything worked, you should have a Debug or Release directory with a beautiful libcef.so library in it.