This study provides the first detailed information on the migration routes and stopover sites for the endangered Scaly-sided Merganser (Mergus squamatus) breeding in Northeast China. Scaly-sided Mergansers (n = 4) were tagged with Platform Transmitter Terminals at Dailing in the southeastern Lesser Xingan Mountains of China during the late breeding seasons of 2010 and 2011. Two Scaly-sided Mergansers completed their autumn migration across the Yellow Sea, lasting 58 and 26 days, respectively, arriving on their wintering grounds at Yuanjiang River in Hunan Province and Xiushui River in Jiangxi Province of China. Both of the Scaly-sided Mergansers stopped at four sites and travelled 2,600 km from their breeding to wintering grounds. After a stay of 120 days, one of the marked individuals departed its wintering ground and returned to Dailing on 19 April 2012 and used a similar route as that in autumn migration and stopped at two sites. Wetlands at Ryonghung Gang estuary in North Korea, Yunshui River and Chidong Lake in Hubei Province of China, and Songjiang River in Jilin Province of China were used as major stopover sites. The determination of previously unknown wintering grounds and stopover sites in China and North Korea provides opportunity to discover more populations of the Scaly-sided Merganser outside its breeding areas.