Efficiency analysis of the Partner Organizations can benefit all the microfinance sector's key stakeholders to benchmark the current scene and formulate optimal policy agenda. This study seeks to measure the partner organizations of the Pakistan Poverty Alleviation Fund's social and financial efficiency and to identify causes and sources of their inefficiencies. A non-parametric technique known as Data Envelopment Analysis is applied to investigate the Partner Organizations' efficiency throughout 2005-2015. The required data was obtained from the database of the Mix-Market and Pakistan Microfinance Network. The social and financial efficiency was estimated assuming Constant Return to Scale, Variable Return to Scale, and with respect to the Operational Scale of the Partner Organizations. Results revealed that the partner organizations are more scale efficient (median = 75%) than pure technically efficient (median = 55%). Further, graphical representations show a decreasing linear trend and negative serial correlation in the percentage of efficient partner organizations. The model fit results show that institutional characteristics that influence partner organizations' efficiencies significantly include their age, Operational Self-Sufficiency, personnel, loan officers, assets and debt. Finally, the diagnostic tests for endogeneity, heteroskedasticity, heterogeneity, and cross-sectional dependence were performed.