Surface velocity observations of the eastern part of the Tsugaru Strait made by the high-frequency radar revealed frequent occurrence of frontal waves along the axis of the Tsugaru Warm Current in 2017–2019. The current axis (maximum of the zonal velocity in the meridional direction) disturbed in the north–south direction with period of ~ 13.7 days that is dominant timescale of tide modulation in the strait, in addition to that of ~ 27.3 days. The amplitude of the axis fluctuation increased in the downstream direction, from the eastern neck of the channel (~ 141.0°E) to the outlet of the strait adjacent to the Pacific Ocean (~ 141.5°E). The propagation speed of the disturbance was slower than that due to surface advection especially in the seasons when the stratification was developed, and agreed well with that estimated from the theory based on the two-layer baroclinic instability model except for winter. The north–south modulation of the axis at the outlet of the strait (~ 141.5°E) could cause short-term (from 20 days to 1 month) variations of an anticyclonic gyre of the Tsugaru Warm Current that is developed in the east of the outlet from summer to autumn reported by the previous studies.