The Braves could manage just 16-48 field goals for 33 percent, and were 4-12 for three-pointers, and just 5-16 from the free throw line.
Emmetsburg made 27-55 shots for a warm 49 percent, and netted 11-19 free throws.
Eric Wilkie paced Cherokee's scoring with 15 points, while Jake Spindler tallied nine, and Zac Smith seven. Smith led the Braves on the boards with eight rebounds.
"We didn't have a very aggressive first half," said Cherokee coach Bob Lee. "Emmetsburg sat back in a 2-3 zone defense and we made poor passes.
"We felt like we increased our energy and effectiveness in the second half, but still struggled to get the ball in the hoop.
The Braves end regular season play with a 3-16 record.