Graham was signed to the Pirates on December 3, 2001 and eventually rose to be the senior director for player development. In that position, he coordinated instruction and oversaw the signing of free agents, staffing, budgets, player movement, affiliate relationships and the Latin American field operations. In addition, he installed and implemented a system of individual player plans which provided instruction and resources to insure the individual development of every Pirate player. Under Graham, the Pirates minor league teams finished with a combined winning percentage above .500 in four of his five seasons. In 2002, the Pirates were honored as the Topps' Baseball “Organization of the Year.”