Before joining the Greater Middlesex Conference for the 1998-99 boys basketball season, Middlesex had always been a fixture in Mountain Valley Conference hoops. The Blue Jays have garnered only three 20-win seasons in its school history.
Led by head coach Gary Feath, Middlesex reached the 1993 Central Jersey Group 1 final and then won its only sectional title in 1994. Feath’s sons, Brian, the Jays’ all-time leading scorer, who later coached another Blue Jays squad to 20-win season in 2008-09, and Kevin teamed up with the likes of B.J. Reilly during that two-year period in the early to mid 90s.
| Season | Wins | Losses | Win % |
| 1992-93 | 21 | 4 | 0.840 |
| 2008-09 | 21 | 7 | 0.750 |
| 1974-75 | 20 | 6 | 0.769 |