The 35-year-old, who has worked on the ITV breakfast show for ten years, will not renew his contract and is in discussions about new projects.
"Ben's two-year contract with GMTV is up at the end of April," reads the statement.
"Earlier this year, his management made it clear that he would not be renewing it, but would be happy to stay on temporarily during this transitional period.
"Ben is excited about moving on after ten incredible years and will be focusing on a number of new projects with ITV and other channels."
The One Show's Adrian Chiles was revealed as a new host on the GMTV sofa earlier this week. GMTV newsreader Helen Fospero has been tipped to join him on the sofa later this year.
Shephard is the third presenter to depart GMTV in the last 12 months, following Penny Smith and Fiona Phillips's exits. Tabloid reports have speculated that Andrew Castle, Emma Crosby and Kate Garraway may also be leaving the show.