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Abstract Background There is limited evidence from community-based interventions to guide the development of effective maternal, perinatal and newborn care practices and services in developing countries. We evaluated the impact of a low-cost package of community-based interventions implemented through government sector lady health workers (LHWs) and community health workers (CHWs) of a NGO namely Aga Khan Health Services on perinatal and neonatal outcomes in a sub-population of the remote mountainous district of Gilgit, Northern Pakistan. Methods The package was evaluated using quasi experimental design included promotion of antenatal care, adequate nutrition, skilled delivery and healthy newborn care practices. Control areas continued to receive the routine standard health services. The intervention areas received intervention package in addition to the routine standard health services. Outcome measures included changes in maternal and newborn-care practices and perinatal and neonatal mortality rates between the intervention and control areas. Results The intervention was implemented in a population of 283324 over a 18 months period. 3200 pregnant women received the intervention. Significant improvements in antenatal care (92% vs 76%, p < .001), TT vaccination (67% vs 47%, p < .001), institutional delivery (85% vs 71%, p < .001), cord application (51% vs 71%, p < .001), delayed bathing (15% vs 43%, p < .001), colostrum administration (83% vs 64%, p < .001), and initiation of breastfeeding within 1 hour after birth (55% vs 40%, p < .001) were seen in intervention areas compared with control areas. Our results indicate significant reductions in mortality rates in intervention areas as compared to control areas from baseline in perinatal mortality rate (from 47.1 to 35.3 per 1000 births, OR 0.62; 95% CI: 0.56-0.69; P 0.02) and neonatal mortality rates (from 26.0 to 22.8 per 1000 live births, 0.58; 95% CI: 0.48-0.68; P 0.03). Conclusions The implementation of a set of low cost community-based intervention package within the health system settings in a mountainous region of Pakistan was found to be both feasible and beneficial. The interventions had a significant impact in reduction of the burden of perinatal and neonatal mortality. Trial registration This study is registered, ClinicalTrial.gov NCT02412293 .