Dr Paniappan Rajmohan will appear in Birmingham Crown Court in May, charged with "conspiracy to procure poison to be used with intent to procure abortion".
Mr Rajmohan was filmed at Calthorpe Clinic in Edgbaston, Birmingham, during an investigation by the Daily Telegraph newspaper.
In the film, Dr Rajmohan is alleged to have agreed to the gender-based abortion.
Prosecutors ruled it was "not in the public interest" to charge Dr Rajmohan, but a private prosecution was brought against him by pro-life campaigner Miss Aisling Hubert, 21, who's being supported by the Christian Legal Centre.
The General Medical Council suspended Dr Rajmohan from practising in 2012.
Earlier this month, 73 MPs from different political parties jointly put forward an amendment to the Serious Crime Bill, to ensure there no legal loopholes allowing abortion on the grounds of gender.
The amendment is still going through Parliament.