An improved efficient stove is the mainstay intervention to reduce household air pollution (HAP) associated with biomass fuel use. It potentially addresses the adverse health outcomes by reducing smoke exposure, fuel consumption, and cooking time. This study evaluated two stove intervention programs and compared them for health effects (respiratory and eye symptoms, lung function, blood pressure and burns) among women who were the main cook of the household. A total of 83 and 134 improved and 209 and 179 traditional stoves in Sindh and Punjab provinces of Pakistan, respectively, were evaluated after 3 months of installation, during June to September, 2014. Twenty-four-hour particulate matter (aRR 0.16, CI 0.11, 0.22), chest tightness (aRR 0.23, CI 0.17, 0.31), attack of asthma (aRR 0.33, CI 0.22, 0.49) (p < 0.001), sandy eyes (aRR 0.63, CI 0.47, 0.97), and itching in eyes (aRR 0.62, CI 0.41, 0.95 (p < 0.050) were present. While in Punjab program, risk reduction for phlegm (aRR 0.60, CI 0.45, 0.81) and protection from burns (aRR 0.56, CI 0.34, 0.91) were observed among women. Mean peak expiratory flow was higher among women using improved stoves in Sindh program (31.58, CI 17.90, 45.25 L/min) only. Overall, the positive health impact was greater among those women using closed kitchens. Interventions with improved stoves can have favorable health impact among women. However, variations in health gains were noted among the two programs, as well as greater impact among women using closed kitchen.