Blackburn - who has been working as the ITV1 drama's story editor since 2009 - takes up the post with immediate effect and will chair his first long-term story conference this week.
The programme's new showrunner succeeds the late Gavin Blyth, who passed away last November following a short period of ill health. Blyth had steered a successful revamp period for the programme, introducing new characters and families and overseeing acclaimed storylines.
Speaking of his new position, Blackburn commented: "This job is very special to me because producing is the ultimate form of storytelling and I've always been very passionate about drama in my working life.
"This is without doubt the most exciting day of my career. I feel a massive responsibility as well as excitement. We'll never be complacent at Emmerdale as it's important we look forward. Together with the cast and crew, we'll continue to work extremely hard to improve what Gavin had started."
Blackburn's first association with Emmerdale came 13 years ago when he joined the soap as a storyliner. He later went on to work on Sky's Dream Team, ITV1's The Bill and BBC One's Ballykissangel among others.
He returned to the world of soap five years ago when he took on the post of story editor at Coronation Street, where his working relationship with Gavin Blyth began. Consequently, when Blyth became Emmerdale's series producer in 2009, Blackburn was invited to re-join the show's team as story editor.
Discussing Emmerdale's future, John Whiston, ITV Studios' creative director for soaps, said: "Stuart Blackburn has a unique combination of the perfect pedigree and the fire in his belly to take Emmerdale to new heights.
"I'm really glad he threw his hat into the ring for the producer's job and I'm confident the show will now build not just on the foundations that Gavin laid but also on the amazing work that [assistant producer] Tony Hammond and the team have done to carry on Gavin's legacy."