Applying to Professional Masters Program after Working with Low Undergrad GPA I am looking to apply for a professional masters program in computer science (M.E. in Computer Science) that is designed to for the working software engineer. It is not advised for those interested in doing computer science research in academia. I have been looking at universities that offer this professional masters degree, and limiting it to ones that have a fully online degree. I plan on applying to most of them.

I have been working full time as a software engineer since I graduated with my B.S. in Computer Science (Graduated in May 2015). I now have 3.5 years of work experience and I am highly regarded by management and coworkers. I have been critical in ensuring the success of multiple projects. I have also excelled at learning all sorts of new things as part of my profession. 

Unfortunately, I graduated with a pretty low undergraduate GPA (Mine was 2.62). There are a variety or reasons for this: dealing with a life threatening illness that impacted me for multiple semesters, a curriculum that was more challenging than nearby universities, a second B.S. degree (Mechanical Engineering) in a subject I am nowhere near as good in compared to software engineering.

My hope is that by working as a very successful software engineer, I can counteract my low undergraduate GPA. Is 3.5 years long enough to reduce the importance of my undergrad GPA when applying for a professional masters? Should I wait longer (like 5, 7, 10 years)? Is there anything else I can do to help address this negative? Thanks!
It depends. It all comes down to the program you are applying to and how much they rate your undergrad GPA vs work experience in the process. Just because the program guide or website says that you should have a 3.0+ GPA from a related undergrad field doesn't mean that it's necessarily a hard and fast requirement. 

I was in a very similar situation and was rejected at my first application, but there was the possibility to appeal the rejection. I called and talked with what would eventually be my adviser and was allowed to reapply with 2-3 letters of recommendation from senior co-workers (you might want to do this at the first application) and allowed into the program on a probationary period. I had to complete a set of undergrad level comp sci maintaining a B (3.0) or higher GPA before being admitted to the starting the MS level courses.