The tremors lasting a few seconds occurred at 12:16 am in border areas of Pithoragarh district, Met office Director Anand Sharma said.
The epicentre of the quake measuring 3 on the Richter scale was located 30.2 degree North and 80.1 degree East.
Slight intensity quakes are frequent in Uttarakhand, parts of which fall into seismic zones IV and V, he said.
A 2.5 magnitude temblor had hit Uttarkashi district in the state recently.