Indian Mujahideen co-founder Yasin Bhatkal and his associate were flown to Delhi by a special plane from Patna on Friday afternoon.
The special plane with Bhatkal and his associate Osadulla Akhtar alias Haddi and NIA officials took off from the Jai Prakash Narayan International Airport at 12.38 p.m.
Earlier the duo, with their faces covered, were brought to the airport from the Bihar Military Police (BMP) camp under tight security.
A small group of people raised slogans at the airport demanding capital punishment to Bhatkal and Akhtar.
The NIA had, on Thursday, obtained a three-day transit remand for the duo from a Motihari court.
The two, who were brought to Patna from Motihari by road on Thursday night, were kept at the BMP campus near the airport.
NIA officials interrogated Bhatkal and Akhtar at the BMP office again on Friday morning before taking them to Delhi.
A joint team of Bihar police and NIA had arrested Bhatkal and Akhtar, carrying a reward of Rs. 10 lakh each, from Nahar chowk in Raxual along the Indo-Nepal border, about 225 km from Patna on Thursday.