The Bantams have spent the season challenging for a playoff spot in League One and remain in sixth position in the standings.
However, the Yorkshire club have suffered five consecutive defeats in the league - six in all competitions - and the decision has been made to part ways with the Scot.
A club statement read: "This decision has not been taken lightly, and this is a sad day for everyone involved. We would like to place on record our sincere thanks to Stuart, who joined the club at a difficult time and restored the fans' belief when the odds were much against us.
"Unfortunately, we have now suffered six straight defeats and the last two fixtures in particular have not brought about the positive change in performances or results that we all hoped for.
"We believe that our current squad is capable of performing to a much higher standard than we have seen recently. We must all accept responsibility for the recent poor run of form, including our players who now have the opportunity to put it right.
"As such, we believe that a change is in the best interests of the club at this time in order to give us the best chance of finishing the season strongly."
McCall leaves Bradford having recorded 44 wins and 24 draws from his 96 games in charge.