Baker is leaving to concentrate on her writing after signing a two-novel deal with publisher Orion.
Under her editorship, Company was the fastest-growing women's magazine in 2002, increasing 26.5% year on year. In the latest ABCs for January-June 2003, it had stabilised, rising 0.1% period on period to 330,617.
She was also behind the National Magazine Company title's revamp in July this year, when it shrunk from British A4 to American A4 size, in response to the runaway success of the handbag-sized Glamour, published by Conde Nast.
"I will be extremely sad to leave Company and my wonderful team. I have very much enjoyed my time at NatMags, but after five fantastic years on Company I am ready for a new challenge and this is something I have always wanted to do," she said.
Baker's leaving date has not yet been confirmed and she will continue in the role until a successor is appointed.
Justine Southall, publishing director of Company, added: "Sam's contribution to the success of Company can not be underestimated and while I will be very sorry to see her go, both on a personal and professional level, I wish her the best of luck."
Baker joined Company from Emap's Minx, which she was made editor of in 1997.
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