Whalan is a city in Fillmore County, Minnesota, United States. The population was 63 at the 2010 census. Whalan was laid out in 1868. I…Whalan is a city in Fillmore County, Minnesota, United States. The population was 63 at the 2010 census. Whalan was laid out in 1868. It was named after John Whaalahan, the original owner of the town site. Whalan was incorporated in 1876. A post office was established at Whalan in 1869, and remained in operation until it was discontinued in 1993.