The Hertfordshire club were in the League One play-off places earlier in the season but have slipped to 15th in the table after losing 13 of their 18 games since December.
Captain Mark Roberts has been named as caretaker-boss until a permanent appointment can be made.
His first game in charge will be the trip to Tranmere on Sunday.
"It's always difficult when you have to replace the man in charge. Gary has done his best but the performances and results over the past few months have been worrying in the extreme," Stevenage chairman Phil Wallace told the club's official website.
"After a very promising start with a new squad, we have slipped alarmingly and the board are concerned that the present management team may be unable to deliver the clubs vision of increasing attendances and developing players in a winning environment.
"We have waited longer than most others in similar circumstances, but we cannot in all good conscience continue to watch this downward spiral and do nothing.
"It's time for a change and we'll see who applies for the position.
"Meanwhile, I'm indebted to skipper Mark Roberts who will, once again, step up and take charge whilst our search takes place."
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