The Middle School at New Covenant Christian School consists of Sixth through Eighth grades. Students begin the transition into the high school by learning Pre-algebra and taking a specialized science class in the Sixth Grade. Seventh and Eighth Graders attend courses conducted by qualified educators in each subject area of Arithmetic, Science, Language Arts, and Social Science. Each curriculum is selected for its academic excellence.
Most recent Stanford Achievement Scores for NCCS:
| Actual Grade Level |
NCCS Students' Avg. Reading Grade Level |
NCCS Students' Avg. Math Grade Level |
| 6th Grade | 10.1 | 9.6 |
| 7th Grade | 10.5 | 10.8 |
| 8th Grade | 13 (college level) | 10.5 |