Colin Ferrie, 52, of Waters Walk, Apperley Bridge, Bradford has also been charged with possessing a class C drug.
He will appear at Leeds Magistrates' Court on 18 August alongside Scott Pendlebury, of Daisy Fields, Bradford, who is charged with the same offences.
It follows claims made by the Mail on Sunday newspaper last year about Dr Ferrie's alleged drug taking.
West Yorkshire Police said a 23-year-old man, from Bradford, who was also arrested as part of the investigation, had been released from bail and would face no further action.
Another man who was interviewed under caution after voluntarily attending at a police station will also face no further action.
Leeds Teaching Hospitals NHS Trust said Dr Ferrie, a consultant paediatric neurologist specialising in epilepsy, no longer worked there.
A former children's doctor from Leeds General Infirmary has been charged with possession of cocaine.