Study of spatiotemporal dynamics of temperature is vital to assess changes in climate, especially in the Himalayan region where livelihoods of billions of people living downstream depends on water coming from the melting of snow and glacier ice. To this end, temperature trend analysis is carried out in Narayani river basin, a major river basin of Nepal characterized by three climatic regions: tropical, subtropical and alpine. Temperature data from six stations located within the basin were analyzed. The elevation of these stations ranges from 460 to 3800 m a.s.l. and the time period of available temperature data ranges from 1960–2015. Multiple regression and empirical mode decomposition (EMD) methods were applied to fill in missing data and to detect trends. Annual as well as seasonal trends were analyzed and a Mann-Kendall test was employed to test the statistical significance of detected trends. Results indicate significant cooling trends before 1970s, and warming trends after 1970s in the majority of the stations. The warming trends range from 0.028 ∘" style="position: relative;">∘C year−1" style="position: relative;">−1 to 0.035 ∘" style="position: relative;">∘C year−1" style="position: relative;">−1 with a mean increasing trend of 0.03 ∘" style="position: relative;">∘C year−1" style="position: relative;">−1 after 1971. Seasonal trends show highest warming trends in the monsoon season followed by winter, pre-monsoon, and the post-monsoon season. However, difference in warming rates between different seasons was not significant. An average temperature lapse rate of −0.006 ∘" style="position: relative;">∘C m−1" style="position: relative;">−1 with the steepest value (−0.0064 ∘" style="position: relative;">∘C m−1" style="position: relative;">−1) in pre-monsoon season and least negative (−0.0052 ∘" style="position: relative;">∘C m−1" style="position: relative;">−1) in winter season was observed for this basin. A comparative analysis of the gap-filled data with freely available global climate datasets show reasonable correlation thus confirming the suitability of the gap filling methods.