The school's first year was 1994-1995 originally in Le Sueur, Minnesota.
In 1995 students discovered deformed frogs at a pond at the Ney Nature Center. The frogs were researched by scientists to discover the reason for the deformity. It was never decided was caused the frogs to be deformed.
MNCS was moved to Henderson in 1998 with a brand new building.
MNCS expanded from 6-12 to k-12 in 2013. 
^ Guernsey, Lisa; Harmon, Sonia. "America's Most Amazing Schools - Minnesota New Country School - Henderson, Minnesota". Ladies' Home Journal. Meredith Corporation. Archived from the original on July 25, 2011. Retrieved April 18, 2011.