The challenge flag in football is a red cloth marker, similar to the yellow penalty flag, thrown by the head coach to trigger a challenge and review of the previous play, called a coaches challenge. Each team gets two challenges per game, but are granted an additional third challenge if the other two challenges are used successfully. A challenge may only be used if the challenging team has at least one timeout, as the penalty for an unsuccessful challenge is the loss of a timeout. A challenge may only be issued about the previous play and a challenge may only be successful if the review presents "incontrovertible video evidence" that the call on the field was incorrect. After a challenge, the referee will announce if the previous call is confirmed or reversed.
If there is a turnover, a scoring play, or any questionable play while the game clock is under 2-minutes or in overtime, the coach cannot call for a challenge. Instead, the replay assistant in the press box can notify the on-field referees of any plays that they believe should be reviewed.
In the NFL, only certain plays or actions can be challenged. For example, a coach cannot challenge that a penalty should've been called on a player, but they can challenge the spot of the ball after the play was over.
Here's a list of every play that can be challenged in the NFL.
Challenges are especially useful when a team feels that they've been cheated due to a call on the field. Challenges are most often called about ball placement, as scoring plays and turnovers are now automatically reviewed by the referees. For example, an offensive team who believes they reached the 1st down marker but the ball was placed short can call a challenge and force the referees to review the play. The defensive team can do the exact same thing if they believe that the offensive team did not reach the marker but were given a 1st down.
Challenges can backfire. For example, if a coach challenges the placement of the ball and the review reveals that the team had more than 11 men on the field, the team can be assessed a penalty. They will receive an additional timeout however, if the review was 'successful,' meaning a change was made to the original calling on the field.
A challenge cannot be called on a play if another play has already occurred. Challenges can only be called on the previous play from scrimmage. If a penalty occurs before the next snap, a challenge can still be called on the previous play as the snap has not occurred, thus the next play has not begun.
The NCAA and CFL have slightly different rules regarding the challenge system.
The CFL is modeled largely after the NFL challenge system, with few differences. Most differences involve certain plays that normally don't occur mutually between the two leagues, such as running forward towards the line of scrimmage before the snap in the CFL. The major difference is that CFL teams are only allowed one challenge per game. Like the NFL, the team must have a timeout available to use for the challenge.
The NCAA is also modeled after the NFL. However, the NCAA has more flexible rules when it comes to the review system. Therefore, most plays in the NCAA can be reviewed. NCAA teams are allowed one challenge per half and they must have an available timeout. If their first challenge is successful, they keep their timeout and are given an additional challenge. Teams may only challenge twice per half at max. There is also no physical challenge flag in the NCAA.