Allan becomes only the third sales director in Channel 4's history, replacing Andy Barnes, who stepped down in April after 14 years in the role.
Reporting directly to Channel 4 chief executive David Abraham, Allan will be responsible for delivering around £1bn in annual revenues by leading a 200-strong sales team across agency sales, airtime management, sponsorship, ad-funded programming and product placement. He will also take a seat on the Channel 4 board.
Allan joined OMD in 1995 as a graduate TV buyer, and was promoted to TV director at the age of just 26. He became deputy managing director in 2005 and took charge of the firm in 2007, aged 32.
Commenting on the appointment, Abraham said: "Jonathan is an outstanding leader with enormous potential and I am delighted to be welcoming him to the Channel 4 executive team in the role of sales director.
"He has achieved an impressive amount in his career to date, and has considerable client facing skills, as well as a track record in digital innovation. This is a crucial role at the heart of Channel 4's future strategy, and I am confident he will rise to the challenge."
Allan added: "I have worked with Channel 4 as both client and media partner for many years, so I am extremely excited to be given the opportunity to shape and direct the sales team to maximise its revenue potential. I've had a fantastic career with brilliant people at OMD UK, but I could not resist the opportunity that this role, brand and institution represents."
Last summer, Channel 4 agreed a ten-year deal to handle ad sales for UKTV's digital channel portfolio, including Dave, Eden, Yesterday and Good Food.