Short answer: If it's valid, verifiable work that you did, then definitely add it!
There is no harm in adding the work you did for a non-profit on to your CV. If there were skills you learned or expanded on, and goals you achieved, and potentially someone who can act as a reference for your work, then there is absolutely value in including it.
Make sure that you show on your CV the technologies you used, the type of analytical work you may have performed, what you completed and what benefits it brought to the non-profit organisation.
Story: A few years ago I was doing development work for a non-profit after hours. It allowed me to expand a skillset that I wanted to gain some practical experience in, and the person I was working for has on occasional acted as a reference for me :)
I misinterpreted your situation that you did work directly for the non-profit, rather than in your regular role that the company you work for, your company provided services to them. My answer pertains to the former situation, not the latter.
If it was just a part of your normal job, you should not mention separately. At best you could add a line to the duties for your current employer such as, "we provided services for xxx non-profit organisation". However, as Joe Strazzere states in his answer, be very careful about non-disclosure.