Bob Blair was a soldier, so the young Wayne moved around. While Blair was still young, his father was posted to Woodside in South Australia, then when Wayne was a teenager his family was sent to Rockhampton. In Rockhampton he excelled at cricket and rugby, then later became interested in acting and dancing at school. Blair had a job as a tour guide at Rockhampton's Dreamtime Cultural Centre, where he was also one of the Dancers. He went on to do a marketing degree at CQUniversity Australia, though his elective subjects included Comic Drama and Australian Drama. He briefly went to Sydney to play rugby league for the Canterbury Bulldogs under-21s. After a failed audition for NIDA in 1992, he eventually did a three-year course at the Queensland University of Technology in acting.

Blair's first recorded on-screen appearance was in a 1997 Australian TV film called The Tower. The following year he appeared on All Saints and Wildside. He has also appeared in Water Rats and Fireflies. 1998 was also the year he was one of the first four film makers to be mentored under the Metro Screen Indigenous Mentor Scheme for which he made a short film called Fade 2 Black. Ten years later he was to become a mentor himself under the same scheme.

Blair was nominated for Best Screenplay in a Short Film in 2005, at the AFI Awards for his work on The Djarn Djarns. In 2012, he was nominated for Best Direction for his film, The Sapphires.

In 2007 he starred as Othello for Bell Shakespeare, a show that toured Australia with stops at Sydney, Melbourne and Canberra as well as other cities. He also directed three episodes of Lockie Leonard with a further four in 2010.

In 2008 Blair directed all thirteen episodes of the Australian children's TV series Double Trouble, about twin Indigenous girls separated at birth. In 2009 he wrote an episode of the second season of The Circuit. 2010 saw Blair direct four episodes of the Australian-British children's supernatural comedy TV series, Dead Gorgeous. He directed British-Jamaican Debbie Tucker Green's play Dirty Butterfly and co-directed the biographical play, Namatjira, with Scott Rankin who also wrote the play, both plays at Sydney's Belvoir St Theatre. He was also chosen in the same year as one of the stars of the Sydney Theatre Company's revival of Sam Shepard's True West, directed by Philip Seymour Hoffman.

Wayne Blair was awarded the Bob Maza Fellowship for 2011 by Screen Australia to provide opportunities for career development. 2012 was a big year which saw the making of his hit film, The Sapphires, which brought him recognition around the world with a very positive response at Cannes. Later in the year he starred in three episodes of the ABC's TV drama series, Redfern Now and directed another of the episodes. To finish the year Blair was included in Variety Magazine's top ten Directors to watch in 2013.