Reynolds was laid off from WotC in 2002, and afterwards formed his own self-publishing company, "Sean K Reynolds Games." He continued to freelance in the d20 industry while working as an IP developer at Upper Deck. Reynolds was let go from Upper Deck in 2008 and contacted Erik Mona at Paizo Publishing looking to do freelance work, and learned there was a job opportunity due to developer Mike McArtor leaving. In July 2008, Paizo hired Reynolds as a developer on the Pathfinder Roleplaying Game. Jason Bulmahn has described him as a "critical part of the design team". In March 2014, Sean left Paizo, so that he could move to Indiana with his wife.
The Forgotten Realms Campaign Setting won the Origins Award for Best Role-Playing Game Supplement of 2001. It made the Amazon.ca bestseller list at number 47 in September 2002. Reynolds identified the Forgotten Realms Campaign Setting as his favorite individual product from throughout his career, stating that it "was a huge amount of work but was so worth it because it is a great product". In May 2003 his book Races of Faerun (co-authored with Matt Forbeck, James Jacobs, and Eric L. Boyd) landed on the same bestseller list at number 42.