She is a member of the Scottish sextet, Dòchas, who were voted winners of Best Newcomer award at the Scots Trad Music Awards in 2004, where Fowlis herself was nominated for the Best Gaelic Singer award. In 2005, Fowlis released her first solo album Mar a Tha Mo Chridhe (As My Heart Is). The album was produced by Iain MacDonald and Fowlis and instantly gained her worldwide acclaim. It was the busiest year until then in her career, having also released a new album with Dòchas. Fowlis has travelled worldwide with the group and as a solo artist with her own live band.
Her second solo album Cuilidh was released in March 2007, becoming a worldwide top-seller in the Traditional and World Music charts. Her album is a collection of songs from her native North Uist home. Her husband, Éamon Doorley plays fiddle on the album and is a member of Irish traditional group Danú.
Fowlis won the Horizon award at the 2006 BBC Radio 2 Folk Awards, won Folk Singer of The Year at the 2008 awards and was nominated for the Folk Singer of the Year award at the 2007 awards. She appeared on Later With Jools Holland on BBC Two on May 25, 2007, and performed Hùg air Bhonaid Mhòir on the show. Notable fans of Fowlis include Björk, Ricky Gervais and Radiohead's Phil Selway.
In 2008, Julie recorded an album with long-time friends and collaborators Muireann Nic Amhlaoibh, Ross Martin and husband Éamonn Doorley. The album, entitled 'Dual' is due for release in November 2008. Fowlis also toured extensively around Scotland, Ireland, central Europe and America and launched both her solo albums while on tour. Fowlis recorded a version of 'Blackbird' for Mojo Magazine to celebrate the anniversary of The Beatles 'The White Album'. The song, performed in Scottish Gaelic is to be released as a stand-alone single later in the year.