Pakistan is a frontline ally of the US in its Global War on Terrorism. After the 9/11 terrorist attack, the military regime was compelled by Washington to join the US effort to dismantle the Taliban-Al Qaida terrorist infrastructure in Afghanistan and Pakistan that successive regimes had nurtured. While the Pakistani military regime’s cooperation is deemed to be crucial for the success of the US counter-terrorism strategy, there appear to be growing strains and challenges that give rise to fundamental questions about the outcomes of such cooperation. This is clearly seen in the revival of the Taliban and the continuing activities of terrorist and militants group based in Pakistan, the increasing anti-American backlash among segments of the Pakistani and Afghan populations, and the electoral gains made by the Islamist parties in Pakistan. The US-Pakistan counter-terrorism efforts clearly suffer from myriad short comings. Alternative approaches by the United States that move beyond engaging the Pakistani military alone focus on the civilian sector are necessary if the goals of counter-terrorism are to be achieved in the rigon.