Joanna Werner's first credit as a producer is believed to be the 15 minute short film by Ben Chessell, Heartworm (2003). Two years later she was engaged as Assistant Producer on the children's television series Scooter: Secret Agent (2005) and Wicked Science (2005). Between 2007 and 2008 Werner produced the children's series The Elephant Princess (for Jonathan M Shiff Productions), followed by the second series of H2O- Just Add Water (also produced with Jonathan Shiff). The series won the 2009 Logie for Most Outstanding Children's series, was nominated for an AFI Award and won the Nickelodeon Kid's Choice Award for Most Popular Children's series. H20 has since gone on to be a international success selling to over 130 territories worldwide including Nickelodeon in the US. It has also been translated into over 20 languages.
In 2008 Werner established Werner Film Productions. The company's first offering, Dance Academy, is a 26 part live action teen drama series co-produced with ABC Television, ZDF (Germany) and the Australian Children's Television Foundation.
Among Werner's other career credits to 2010 are the 50 minute telemovie The Heartbreak Tour (SBS Television) and the first series of H2O (as associate producer).