Jackson Junction is a city in Winneshiek County, Iowa, United States. The population was 37 at the time of the 2020 census. Jackson Junction i…Jackson Junction is a city in Winneshiek County, Iowa, United States. The population was 37 at the time of the 2020 census. Jackson Junction is located at 43°6′25″N 92°2′48″W / 43.10694°N 92.04667°W. According to the United States Census Bureau, the city has a total area of 5.99 square miles, all land.