After graduation, he pursued a writing career. He worked on Capitol Hill and then briefly for several New York City publications, including Town & Country and Interview magazine. On the advice of some of his friends, he studied at the Neighborhood Playhouse, was coached by Gerald Gordon, and then moved back to Los Angeles in 1994 to pursue an acting career.
Flanigan took two prizes in the Waterkeepers' Alliance downhill skiing competition at Lake Louise in January 2006, an event fellow Stargate lead Richard Dean Anderson has attended as well. He currently resides in Malibu, California.
In September 2007, scifi.com's SciFi Wire Service reported that, "Talent agency UTA filed suit on Sept. 24 against Stargate Atlantis star Joe Flanigan in Los Angeles Superior Court, claiming that the actor owes $99,225 in commissions, according to The Hollywood Reporter; Flanigan's manager, John Carrabino, told the trade paper about the lawsuit: 'I had no idea they did this. This is the first time I'm hearing about this.'" UTA filed a similar lawsuit against actor Wesley Snipes who was equally surprised. This suit was settled in December 2008.
Flanigan features in the contemporary public artwork, Metascifi (2015) by Artist Martin Firrell. Metascifi presents social comment, and philosophical truths about living well, derived from observation of popular American television science fiction. The project features performers and characters from Stargate, Star Trek, Farscape, Firefly and Warehouse 13.
As the ‘meta’ element of the title suggests, the artwork invites Flanigan to comment on the wider social and narrative significance of his Stargate Atlantis character John Sheppard. Most notably, he speaks about the sexual attraction of the archetypal action hero, suggesting it is the impression of the hero’s agency in the world that underpins people’s attraction to characters of John Sheppard’s nature.
