Her departure coincides with a number of changes at the commercial operations of the group, including the promotion of two staff as it looks to beef up its celebrity magazines.
Stephenson, a high-profile recruit from SkyMag, where she worked as advertising director, left last week and will not be replaced, according to the group.
As part of the reshuffle, Helen Mcgregor, senior sales executive at OK! magazine, has been promoted to the new role of group head on New! magazine.
Meanwhile, Sam How, a sales executive working on New! magazine has been promoted to the new role of group head on OK! magazine.
Both report to Melanie Danks, group head of trading.
Before going to work at SkyMag, Stephenson was advertising director at News Magazines, which she joined in January 2006.
Separately, Northern & Shell is considering bidding for the lucrative contract to distribute newspapers on the London Underground.
Stan Myerson, group joint managing director, Northern & Shell, said the group "is considering its position" regarding the Underground contract, which is held by Metro.
The deal will be put out to tender this autumn.
The company is believed to have long heralded ambitions to establish a foothold in the London free market.
Metro owner, Associated Newspapers, is understood to be paying about £1m a year for the distribution deal - and is thought to be making an annual profit of up to £8m on Metro.
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