The Pioneers started off with a 7-0 lead, but they were not able to come back after allowing 28 unanswered points in Thursday's 42-21 loss at Shawnee Mission Northwest.
Junior quarterback Landry Hodges threw a 62-yard touchdown pass to junior receiver Isaiah Ross only 1:32 in the game, but Shawnee Mission Northwest had touchdowns for 59, 14, 23 and 79 to take a 28-7 lead early in the second quarter.
Senior running back Jason Randall had a pair of touchdown runs for 58 and 18 yards, but the Cougars got an 11-yard run for a score and a 20-yard touchdown run to keep the Pioneers from coming back.
The Cougars used their running attack to pick up their first win of the season. They ran it 41 times for 414 yards and five touchdowns.
Randall had 183 yards and two scores on the ground for Leavenworth.
Hodges went 10-for-19 for 121 yards and a score. Ross caught half of the completions for 83 yards and the early touchdown.
Junior Anthony Hunt led the Pioneers with four tackles.
The Pioneers will be at Shawnee Mission West at 7p.m. on Thursday.