The Topeka Scarecrows played in the CHL starting in 1998 at the Kansas ExpoCenter. They only went 28-38 in their first season, 1998-99, but would still make the playoffs, losing in the first round to the Oklahoma City Blazers. Strangely, they would actually miss the playoffs in their second season despite a much better record of 35-27. Their third and final season in the CHL was marred by legal disputes. The league terminated both the Scarecrows and Border City Bandits franchises with 10 games remaining for breaching financial arrangements with the league. However, the Scarecrows would file a restraining order and finish out their season with a first round playoff exit to the San Antonio Iguanas.
The team would be entered in the USHL the following season, and play two seasons in that league before being sold and moved to St. Louis.