Me and my GF had sex on Nov 26th and she took an ipill (emergency contraceptive) within 24 hours of intercourse. I did not ejaculate in her but as a precaution she took the pill. We haven't had sex since then. On Dec 3rd, she had her periods (normal bleeding). Her next period was delayed, that is on Jan 16th (after 43 days from the previous one, again normal bleeding). She even took a pregnancy test on Jan 15th and it showed that she is not pregnant. Now its been 44 days since her last period and today morning she had some brown discharge and nothing after that. She still has the back pain and uneasy feeling like she normally does during her periods. My question is, is the delay and brown discharge due to the pill or could she be pregnant?

Not unless she had sex with someone else in the meantime.

It's very unlikely that she would have got pregnant at all, considering how you did it and the emergency pill. Two normal periods and a negative pregnancy test show she definitely didn't get pregnant.

Whatever is happening now is not pregnancy.

What could be the reason for the delay and the brown discharge today?

The "morning after pill" which ever one you used, upsets, and changes the time of the period for a month or two.

I will assume she did not check with a doctor afterwards or assume no one read all the warnings that come with it.