He is exiting the network after 11 years, to "pursue other opportunities".
The exec will leave his role at the end of July, but will reportedly continue to support existing projects until the end of the year.
He said in a statement: "My mum used to say 'sometimes you have to know the best time to leave a great party' and what a party it's been. I am blessed to have worked alongside such undeniably world class talent, at all levels, internally and externally, and the party continues - I'm so proud of my amazing team and I can't wait to see the next generation of shows - I know they're going to be very special."
Sky boss Zai Bennett, writing on LinkedIn, noted: "After a hugely impactful, and impassioned, 11 year tenure, Jon Mountague announced that he has decided to leave the business, to pursue further adventures outside of Sky.
"Jon has always led from the front, commissioning and exec producing a host of Sky Original comedies from the likes of In The Long Run (Idris Elba) and Sally4Ever (Julia Davis), as well as Funny Woman (Gemma Arterton) and Brassic (Joe Gilgun) to name just a few.
"Jon is a brilliant business leader and truly embodies what it means to work for Sky. Needless to say, I've appreciated his dedication, unrelenting passion for what he does, and well, his comedy, over the years.
"Thanks Jon for everything - you'll be very much missed around Osterley [the location of Sky's headquarters]. Everyone at Sky wishes you the best for what's next."
Broadcast reports that Sky Studios has not yet decided how best to replace Mountague.