Taylor is setting up a company called Makieworld, which will produce 3D dolls and accessories with educational elements for young girls.
Her exit follows the departure of Channel 4 Education head Janey Walker earlier this year, as part of chief executive David Abraham's management restructure.
In a posting on her Wonderland blog, Taylor wrote: "A lot of folks are going to think I'm crazy, and they'd probably be a bit right. But sometimes, things and timings just happen.
"In my case, I had a magic start-up idea that I actually want to go do, again. I've done this before, and always thought I might want to go back to it."
Taylor also confirmed that Dr Jo Twist would take over her responsibilities at Channel 4 Education, working alongside head of cross-platform Matt Locke.
"I gave C4 a long, long notice period, so I can help them get stuff organised as the place goes through its pretty radical change programme," she wrote.
"Dr Jo Twist will pick up the baton, which I'm obviously over the moon with. She's a towering talent, and all the Education sites, games, telly and apps will be in the best hands in the business."
Taylor added: "I'll miss Education. We have the best team, and we have the most fun I think it's possible to have in a large corporate environment. It's not uncommon to find us screeching with laughter, and walking away from that is really tough.
"I'm fantastically proud of what we've accomplished in the three years of taking Education from a TV-only department to an any-platform, any-format department."
> Click here to read our recent interview with Taylor