The political administration has registered a case against the accused under sections 302 and 419 of Pakistan Penal Code and section 11 of Frontier Crimes Regulation.
A warrant of the case was sent to the superintendent of Peshawar prison.
The administration fixed December 20 for hearing the case inside the jail. Political agent Mutahir Zeb will hear the case.
Afridi, who was arrested immediately after the May 2, 2011 operation by US commandos that killed Osama, was convicted for treason over alleged ties to militant group Lashkar-e-Islam.
On August 29, a judicial official had overturned the 33-year jail sentence of Afridi, who was sentenced in May, 2012 on charges of colluding with the banned militant outfit.
Frontier Crimes Regulation Commissioner Sahibzada Mohammad Anees ruled that a judge in the tribal belt had exceeded his authority when he handed down the sentence last year.
The doctor has filed an appeal for a fresh probe.