On March 28, 2012, Hinson was announced the head coach of Southern Illinois University's men's basketball team.

[1] Hinson inherited a Bears program that had been to the NCAA Tournament Sweet 16 the previous season and featured five seniors, out of seven returnees overall, who were part of that successful squadron.

[1] After amassing a 22–10 record, including 10 wins in their previous 11 games, and ranking with an RPI in the middle 30s, Hinson and his squad were disappointed to be omitted from the (then) 64-team NCAA Tournament field.

However, the National Invitation Tournament (NIT) came calling, and SMS drew a first-round matchup at home with Southern Methodist, whom they defeated handily.

Along the way, the Bears upset #23 Southern Illinois, the Missouri Valley regular season champion, in the conference tournament semifinal game.

Hinson led Missouri State to victory over Rice University in the NIT opener, but succumbed to Davidson in the second round.

The Bears again tasted postseason action, defeating Stanford and Houston in the NIT before getting blown out at Louisville in the tournament quarterfinals.

However, of their 11 losses, five were to MVC foes Creighton and Southern Illinois, and the NCAA Tournament selection committee passed on inviting Missouri State to the big dance.

[8] However, when the season was complete,[9] MSU President Michael T. Nietzel called a press conference to announce that Hinson would remain as head coach.

However, the team's mediocre record heightened speculation about Hinson's future,[8] resulted in the creation of a website advocating his dismissal, Fire Barry!

After the end of the season five players including two starting freshmen Jordan Caroline and Dion Lavender transferred.

Despite being picked to finish ninth in the Missouri Valley, Hinson lead the improved Salukis to early season success with an 11–2 non-conference record.

The Salukis finished tied for fourth in the Missouri Valley regular season before looking overmatched and losing to Northern Iowa in the conference tournament.

However, a weak non-conference schedule and a below average year for its conference meant no NCAA or NIT bid for the team.

On January 20, Hinson picked up his 226th victory while coaching in the Missouri Valley when the Salukis defeated Indiana State University 79–66 at the SIU Arena.