C.C. San Francisco

Ayoob originally attended the City College of San Francisco where he was regarded as one of the best junior college quarterbacks in the nation. He was also a teammate of future Cal player Desmond Bishop.^[4]

Ayoob helped lead the school to a 23-1 record over his two seasons, winning a national championship (12-0) in 2003. In 2004, he was named the state's community college Offensive Player of the year by the JC Athletic Bureau/California Community College Football Coaches Association. He earned First-team JC Gridwire All-America after completing 61.3% (217-of-354) of his passes for 3,679 yards and 35 touchdowns in 2004. He ranked #1 in the state in passing efficiency (177.5) and led the most prolific junior-college offense in California (500.1 yards-per-game). SuperPrep rated him the #2 junior college player in the nation in its postseason JuCo 100. Rivals.com ranked him #15 on its national JC list. He helped lead his team to an 11-1 record, with the team's only loss a 39-32 loss to College of the Canyons in the California state championship game. He was named the Offensive Player of the Game in loss, as he threw for 386 yards and four touchdowns and also rushed for 62 yards on seven carries. In his two seasons at CCSF, he completed 352-of-571 pass attempts (61.6%) for 5,790 yards and 55 touchdowns while rushing for an additional nine touchdowns. He also won the MVP award in the state championship game in each of his two seasons.

Cal

Ayoob then transferred to the University of California, Berkeley. In 2005, he started nine games at quarterback, after an injury to Nate Longshore, and helped lead the Bears to a 5-4 record in those games. On the season, he passed for 1,707 yards with 15 touchdowns. He ended the season #8 in the Pac-10 in passing yards (155.2 yards-per-game) and ninth in total offense (160.5 yards-per-game). His best game of the season may have been at New Mexico State when he was 17-of-26 passing for a season-high 284 yards and one touchdown. He also ran for three touchdowns on his first three carries. His first career start came on the road against Washington where he went 17-of-27 passing for 271 yards with four first-half touchdown passes. Against Oregon State, he became the first Cal player since Kyle Boller in 2002, to catch, run for, and pass for a touchdown in the same game. He threw for 274 yards against Washington State, including 91 in the final seven minutes when he led the Bears to a 42-38 come-from-behind win. He was 4-of-4 with two touchdowns on Cal's last two possessions. He ran for a touchdown and passed for two touchdowns in the 28-0 win over Arizona. He came off the bench to play in the season opener against Sacramento State, where he completed 0 passes out of 10 attempts. He also came off the bench to play the regular season finale at Stanford.

In 2006, Ayoob played in just four games as Cal's backup quarterback to Nate Longshore.^[5] He completed 9-of-22 passes for 187 yards and a 40-yard touchdown pass to DeSean Jackson against Tennessee. He also played against Portland State (2-for-4, 18 yards) and Minnesota (no attempts).

While at Cal, Ayoob majored in Social Welfare.