Malaria is endemic in Pakistan and constitutes a national health priority However the parasite and vectors are showing resistance to common antimalarial drugs and insecticides. The provinces of Balochistan, Sindh and Khyber Pakhtunkhwa and the Federally Administered Tribal Areas have the highest malaria burden. Districts and agencies bordering Afghanistan and Islamic Republic of Iran account for 37% of the malaria burden with an annual parasite incidence (API) exceeding 4.5/1000 population per year. Moreover, there has been a growing risk of Plasmodium falciparum malaria incidence in areas where previously P. vivax was predominant. New and effective control tools have been introduced such as rapid diagnostic tests, artemisinin-based combination therapy and long-lasting insecticide-treated nets. This paper reports the progress achieved in the implementation of a malaria control strategy in Pakistan, shares major outstanding challenges and unearths the potential of performance-based implementation for advancing resource mobilization and collaborative partnerships.