The Middlebury Cross Country teams took part in the 2006 NESCAC Championships hosted by Connecticut College. The Panther women placed fourth in the 11-team event, while the men came in sixth of 11 squads. Amherst won the women's race, while Williams captured the men's race.

Andrea Giddings led the Middlebury women in fourth place with a time of 23:15. Finishing in eighth was Erin Archard with a time of 23:26, followed by Alexandra Krieg in 10th in 23:28. Middlebury's fourth finisher was Claire Schultz in 16th place (24:14), followed by Emily Allison in 33rd (24:51).

Jimmy Butcher paced the men's team once again, finishing the race in ninth place with a time of 26:45. Coming in 26th overall was Will McDonough in 27:01, followed by Bruce Hallett in 32nd with a time of 27:11. Peter Murphy was 36th overall and fourth for Middlebury in 27:16, followed by Chris Pelliccia in 55th (27:46).