1. Copy the zenburn_mod.css file inside the highlightjs's folder.
2. Be sure to replace in the relative .html (e.g. header.html) and setting files (e.g. Doxygen) the default .css with this (e.g. default.css/github.css to zenburn_mod.css)

Note: color list:

3f3f3f -> 1f1f1f #text
8cd0d3 -> 7ee0de #number
dca3a3 -> dc8383 #link
efdcbc -> feb183
e3ceab -> feb183 #keyword
dcdcdc -> dcdccc
efef8f -> dcdccc+bold #title
cc9393 -> e4e792+bold #functions
7f9f7f -> same+italic #comment
string -> dc8383
literal-> keyword
added  -> 00ff00 #diff
delete -> ff0000 #diff

HighlightJS inside Doxygen VS Notepad++ modded version: