The Take That frontman beat Peter Andre to be handed the award, sponsored by Premier Inn.
Barlow stated that winning the award felt "amazing" after previously joking to Andre on Twitter to "stand aside".
"I've been waiting for it for a long time," he told PA. "My kids are really excited and I don't think they can quite believe it.
"Being a dad is a really important part of my life and it means a lot to have won this award."
The singer is father to children Daniel, Emily and Daisy, and his wife Dawn is currently expecting another baby girl.
Jay-Z, Cristiano Ronaldo and David Cameron were also nominated for the award, which is voted for by the public, which recognises fathers who balance life in the public eye with the demands of parenting.
However, British prime minister Cameron's recent revelations that he accidentally forgot his daughter in a pub may have lost him votes for the award.
Andre won the award last year and beat Barlow and Jeff Brazier to the title in 2010.