Leanne Zaloumis, 29, of Catford, south-east London has been charged with aggravated burglary and will appear at West London Magistrates' Court on Monday.
The X Factor judge's £9 million west London home was allegedly broken into at 10.30pm.
Cowell was said to have come face-to-face with the female intruder as he watched television, according to the Daily Mail.
Zaloumis was reportedly found "lying on Simon's bed in his bedroom".
A friend said: "It was a frightening experience. Simon's fine but shaken up - because he didn't expect something like that to happen."
The woman was allegedly able to gain access to the property by entering through a downstairs window.
Cowell's Britain's Got Talent returned to ITV1 last night against BBC One's The Voice UK.
He has said that The Voice UK has provided a "wake up call" to his own shows to remain dominant in the ratings.