The Eels scored 36 points to earn the win despite the Lakers' Anthony Witt taking the individual victory in 15:44.
Clay City won the meet on the back of strong pack running, placing five runners on the All-Conference squad.
Kevin Cook was fourth in 17:42 while teammate Braxton Griffith was sixth, just nine seconds back. Parker Modesitt was seventh in 18:05 with Jessie Vansickle in ninth at 18:20 and Conner Modesitt in 10th overall in a time of 18:39.
Ben Dickey was 12th and Kyle Yocom was 18th overall.
The girls' team event was won by Shakamak by just one point as Linton and North Central each came in with 45 points. The Miners earned second on the strength of a better sixth runner's placing.
The Eels were led by an eighth-place by Andrea Ladd in 23:40 followed by Brittaney Richard in 17th, Stephanie Granger was 19th ahead of Samantha Stoops in 21st and Taylor Walden was 25th.
The Eels will be back in action on Thursday at home against visiting Terre Haute North.
Girls Team Results
Shakamak 44, Linton 45, North Central 45, Clay City 88, no other complete teams
Casey Fougerousse (SH) 20:40
Clay City: 8. Andrea Ladd, 23:40, 17, Brittney Richard, 26:03, 19. Stephanie Granger, 26:53, 21. Samantha Stoops, 27:09, 25. Taylor Walden, 29:52
Boys Team Results
Clay City 36, Shakamak 41, Linton 93, North Central 95, Eminence 112, Union 133
Anthony Witt (SH) 15:44
Clay City: 4. Kevin Cook, 17:42, 6. Braxton Griffith, 17:51, 7. Parker Modesitt, 18:05, 9. Jessie Vansickle, 18:20, 10. Conner Modesitt, 18:39, 12. Ben Dickey, 19:04, 18. Kyle Yocom
1. Andy Shaffer, 20:51, 2. Austin Sinders, 3. Landry Moss