Security, in non-traditional sense, is inclusive and comprehensive concept that covers various facets of human life including public health. But South Asian security agenda has always been dominated by a traditional and state-centric approach, leaving little or no space for non-traditional security issues including but not limited to environmental degradation, repression, hunger and disease. Pakistan is no exception where health security or public health has always remained on the margins of the country’s overall security agenda. Therefore, Pakistan was caught off-guard and ill-prepared when Covid-19 struck the country in February 2020. The current paper seeks to document the impact of Covid-19 on Pakistan’s various security sectors including economic, environmental, societal, and conventional security, government’s response and outcomes. The paper concludes economic fallout caused by corona virus could potentially hit the sectarian and ethnic fault lines of the country hence restricting Pakistan’s conventional options to respond to Indian belligerence during the pandemic. Since pandemics know no boundaries, a joint Indo-Pak cooperative approach on dealing with non-traditional security threats such as Covid-19 will offer a rare window of opportunity to partner in a noble cause to protect billions of South Asians against the modern plague