Abstract Background Malaria and dengue are the two major vector-borne diseases in Mizoram. Malaria is endemic in Mizoram, and dengue was first reported only in 2012. It is well documented that climate change has a direct influence on the incidence and spread of vector-borne diseases. The study was designed to study the trends and impact of climate variables (temperature, rainfall and humidity) in the monsoon period (May to September) and deforestation on the incidence of dengue and malaria in Mizoram. Methods Temperature, rainfall and humidity data of Mizoram from 1979–2013 were obtained from the National Centers for Environmental Prediction Climate Forecast System Reanalysis and analyzed. Forest cover data of Mizoram was extracted from India State of Forest Report (IFSR) and Land Processes Distributed Active Archive Centre. Percent tree cover datasets of Advanced Very High Resolution Radiometer and Moderate Resolution Imaging Spectroradiometer missions were also used to study the association between deforestation and incidence of vector-borne diseases. The study used non-parametric tests to estimate long-term trends in the climate (temperature, rainfall, humidity) and forest cover variables. The trend and its magnitude are estimated through Mann-Kendall test and Sen's slope method. Year-wise dengue and malaria data were obtained from the State Vector Borne Disease Control Program, Mizoram. Results The Mann-Kendall test indicates that compared to maximum temperature, minimum temperature during the monsoon period is increasing (p < 0.001). The Sen’s slope estimation also shows an average annual 0.020C (0.01–0.03 at 95% CI) monotonic increasing trend of minimum temperature. The residuals of Sen’s estimate show that temperature is increasing at an average of about 0.10C/year after 2007.Trends indicate that both rainfall and humidity are increasing (p <. 0.001); on an average, there is a 20.45 mm increase in monsoon rainfall per year (5.90–34.37 at 95% CI), while there is a 0.08% (0.02–0.18 at 95% CI) increase in relative humidity annually. IFSR data shows that there is an annual average decrease of 162 sq.km (272.81–37.53 at 95% CI, p < 0.001) in the dense forest cover. Mizoram in 2012 was the last state in India to report the incidence of dengue. Malaria transmission continues to be stable in Mizoram; compared to 2007, the cases have increased in 2019. Conclusion Over the study period, there is an ~ 0.80C rise in the minimum temperature in the monsoon season which could have facilitated the establishment of Aedes aegypti, the major dengue vector in Mizoram. In addition, the increase in rainfall and humidity may have also helped the biology of Ae. aegypti. Deforestation could be one of the major factors responsible for the consistently high number of malaria cases in Mizoram.