As Sharif began delivering his address at the US Institute of Peace, a prominent independent think-tank here, a protester raised slogans including "Free Balochistan" besides calling him a "friend of (Osama) Bin Laden".
The man was also holding a poster that read "Free Balochistan".
He was taken out of the auditorium by the security forces following the incident that forced the visiting premier, Sharif, to pause briefly and then resume his address.
The army has fought separatist Baloch militants on several occasions during much of Pakistan's existence.
The latest wave of insurgency was triggered after the Pakistan Army, under the direction of the then President General Parvez Musharraf, bombed and killed elderly Baloch tribal chief Nawab Akbar Bugti in 2006.
Pakistan says it is winning the battle against separatists in the restive southwestern province, but Baloch activists say abductions, torture and killings by the army are deepening hostility for the government.