Because he surprisingly started every game in 2016, after coming to the team as a fourth-round project before having one of the finest rookie seasons of any quarterback in NFL history, Prescott earned an extra $353,544.57 via the league's performance based pay bonus system.
The system rewards players for outperforming their contract based on playing time.
The money does not count against the salary cap and the league reimburses the teams for the payments.
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Prescott received a $383,393 signing bonus and a $450,000 base salary last year.
The performance-based pay puts his first year take at $1,183,937.57.
Joining Prescott in taking home big money through the performance based pay system were two other rookies in cornerback Anthony Brown and defensive tackle Maliek Collins.
Brown, a sixth-round pick, played in every game, including nine starts, and received an extra $346,198. Collins picked up an extra $205,873.
Ten Cowboys earned more than $100,000 in performance-based pay.
The others were defensive end David Irving (194,620.41), linebacker Anthony Hitchens ($186,101.52), linebacker Damien Wilson ($184,706.86), receiver Brice Butler ($120,519.52), safety Byron Jones ($118,288.93), defensive end Jack Crawford ($108,420.27) and fullback Keith Smith ($101,733.13).