The duo, played by Cobie Smulders and Neil Patrick Harris, used to date but broke up during the last season.
Bays has now told TV Squad that he does not believe that the couple are over for good.
"What's going on between Barney and Robin is palpable and real and far be it from us to deny it," he said. "It's now just part of the fabric of the show and I think there's definitely a future there."
How I Met Your Mother continues on Mondays at 8/7c on CBS.