Younis Taukali was killed by paramilitary Frontier Corps (FC) near Turbat where 15 bullet-riddled bodies were found on Wednesday, the military's Inter-Services Public Relations (ISPR) said.
The dead hailed from Punjab and were trying to illegally travel to Europe via Iran.
Taukali was one of the top commanders of the separatist Balochistan Liberation Front (BLF) which has been declared a terrorist group by Pakistan.
He was also involved in attacking FC convoys with improvised explosive devices (IEDs) and was wanted for multiple killings, the ISPR said.