Extremely small snow cover in the winter of 2015/16 and interannual variations of snow cover over the Japanese Northern Alps are simulated by a regional climate model with 2 km grid spacing based on the Japanese 55-year Reanalysis (JRA-55). Our simulation well reproduces the daily variation of snow depth along the Tateyama-Kurobe Alpine Route, located at the Japanese Northern Alps, as compared to snow depths observed by time-lapse cameras in 2014/15. Our simulations indicate that the maximum snow depth in 2015/16 was the lowest of 16 years at high elevations, especially in the spring. In March 2016, weak cold air outbreaks and inactive storm-tracks cause little precipitation around central Japan, resulting in greatly reduced annual accumulated snowfall than usual at high elevations. Warmer April conditions also contribute to accelerated snow melting, resulting in the disappearance of snow at high elevations one-month earlier than usual. Analysis of large-scale circulations related to past large El Niño years shows a warmer April is a typical response in El Niño events, while weak cold air outbreaks and inactive storm-tracks are contributed by the extratropical internal variation rather than lingering El Niño effects in tropics.