Gomez won his 2,000th race at Del Mar in August 2002 before encountering personal problems the same year that halted his career as a jockey. Gomez struggled with addiction and was arrested in July of 2003 for possession of a controlled substance. Sentenced to serve 40 days in jail and enter drug rehabilitation, Gomez realized he had serious problems with substance and alcohol abuse. He entered rehab in October 2003, and after missing 21 months of racing to address his personal problems, Gomez finally returned to the track in late 2004 as an underdog.

Working his way back to the top, Gomez won two Breeders' Cup races exactly two years to the day after entering rehab. He was also the number one jockey at Hollywood Park upon his return to the racing world. Gomez had not only tackled his personal demons, he had become the go-to jockey. His successes led to a stint on the East Coast riding as the first jockey for top trainer Todd Pletcher. With Pletcher, Gomez gained his first Kentucky Oaks win on Rags to Riches and won 16 stake races on Pletcher-trained horses, including five grade one races. A record-breaking year followed in 2007 when Gomez became the top jockey in terms of earnings, having amassed more than $22 million. As a result, Gomez was presented with the Eclipse Award for outstanding jockey of the year.