I graduated a year ago with a BA in Economics from a small state school. Due to family issues at the time my GPA really suffered and I graduated with a 2.26 GPA.

I now work for a company that will pay for me to get my Masters degree. Ideally I'd like to get into a top MBA program in about 5 years but I know my poor undergrad GPA is a huge obstacle. I am considering getting a MS in Applied Economics from Southern New Hampshire University to supplement my future application and offset my low undergrad GPA.

What are everyone's thoughts on this? Would getting a Master's degree help with getting into a good MBA program or is it a waste of time?

hey there, I am facing the same issue here. Had rather lower gpa in my undergrad (although above average), while gpa in MA is high (honors), yet I don't think MA gpa matters much. One way to offset a poor undergrad gpa is to score high in the gmat as it was suggested above.
Cheers and study hard

A master's degree could help, but ideally it would be from a top-ranked institution.

I also applied with a relatively low GPA (3.1) in electrical engineering and got a master's in EE from UCLA (4.0 GPA). I ended up getting into Haas and Kellogg. I think the master's helped, but other things that went in my favor include:
1) My 750 GMAT
2) Alternative transcript of A's in classes such as econ and accounting
3) Optional essay where I took responsibility for my low GPA and highlighted more recent indicators of my academic performance

The master's GPA didn't completely make up for my low undergrad GPA, though in combination with my GMAT, it probably helped give adcoms confidence that I could thrive academically in an MBA program.

If your employer is willing to foot the bill AND you are willing to invest the time necessary to really excel at a master's program AND you are genuinely interested in the course material AND you can get your master's from a top institution, then I say go for it. Otherwise, I would agree with the other responses that there are more effective uses of your time.