Female cabin crew, whose uniform features a tight, red skirt, will also now be offered trousers automatically, rather than only when requested.
It said it was a “significant change”.
Newer airlines, such as EasyJet and Ryanair, typically have relatively relaxed rules on uniform, but many longer-established airlines give rules on what make-up must be worn.
The airline’s first uniforms were designed by Arabella Pollen, a 23-year-old designer at the time of its launch in 1984.
She created Virgin Atlantic’s “Virgin Red”. The most recent redesign was by Vivienne Westwood in 2014.Virgin said cabin crew could now work without make-up, but were welcome to follow the palette of lipstick and foundation set out in its guidelines.
Virgin Atlantic spokesman Mark Anderson said: “Not only do the new guidelines offer an increased level of comfort, they also provide our team with more choice on how they want to express themselves at work.”
The airline industry has been among the most conservative when it comes to appearance standards, although it is gradually changing.
British Airways dropped its no-trouser rule for women in 2016, although it still requires female crew to wear make-up.