The Yupik name for the village is Kuinerraq, meaning "new river channel." It has been dated to at least 1000 AD.
Quinhagak is near the Nunalleq archaeological site, which has the "easily the largest collection of pre-contact Yup'ik material anywhere," according to anthropologist Rick Knecht. Thousands of items dating from 1350 to 1670 have been uncovered. These include many organic artifacts preserved in permafrost. The site is located along eroding coastline and up to 75% of the original site is thought to have washed away, , including the original excavation site.