In the Fall of 1988 Indian Hills Elementary opened its doors for the first time. The new elementary was the first school in the Auburn-Washburn school district to have an automated library system. The school housed Kindergarten through 6th grades. The first principal was Victor Dyck, who started his career with Auburn-Washburn at Pauline East Elementary and moved to Pauline Central after East closed. He later taught at Jay Shideler and was the principal at Wanamaker Elementary before moving on to Indian Hills.

Over the years the enrollment continued to grow. By 2007 a bond was passed which approved the building of a new elementary school and the renovation of existing schools. As the new elementary school was being built the district boundaries were recreated. This adjusted the boundaries of Indian Hills and many of its students started attending Farley Elementary School in the 2009-2010 school year.

Indian Hills has not changed much since it first opened its doors in 1988. The school still houses Kindergarten through 6th grades.