| School Name | Grades | Address | Zip | Phone | County | Type | District Name |
| Agape' Christian School | 1, 5, 7, 10-11 | 2713 County Road 220
Middleburg, FL | 32068 | (904) 284-3038 | Clay | private | |
| Annunciation Catholic School | PK-8 | 1610 Blanding Blvd
Middleburg, FL | 32068 | (904) 282-0504 | Clay | private | |
| Black Creek Christian School | 1-12 | 3216 County Road 218
Middleburg, FL | 32068 | (904) 282-4033 | Clay | private | |
| Calvary Christian Academy | PK-12 | 1532 Long Bay Rd
Middleburg, FL | 32068 | (904) 282-0407 | Clay | private | |
| Cinnamon Street Baptist Christian School | K-12 | 29 Cinnamon St
Middleburg, FL | 32068 | (904) 406-5755 | Clay | private | |
| Coppergate Elementary School | PK-6 | 2250 County Rd 209 N
Middleburg, FL | 32068 | (904) 291-5594 | Clay | public | Clay County Public Schools |
| Doctors Inlet Elementary School | PK-6 | 2634 County Rd 220
Middleburg, FL | 32068 | (904) 213-3000 | Clay | public | Clay County Public Schools |
| J.L. Wilkinson Elementary School | PK-6 | 4965 County Rd 218
Middleburg, FL | 32068 | (904) 291-5420 | Clay | public | Clay County Public Schools |
| Lighthouse Christian School Middleburg | 1-12 | 3925 Main St
Middleburg, FL | 32068 | (904) 637-0637 | Clay | private | |
| Madeira Christian Academy | K-12 | 1650 Blanding Blvd
Middleburg, FL | 32068 | (904) 291-1875 | Clay | private | |
| Middleburg Elementary School | PK-6 | 3958 Main St
Middleburg, FL | 32068 | (904) 291-5485 | Clay | public | Clay County Public Schools |
| Middleburg High School | PK, 9-12 | 3750 County Rd 220
Middleburg, FL | 32068 | (904) 213-2100 | Clay | public | Clay County Public Schools |
| Pinewood Christian Academy | PK-8 | 198 Knight Boxx Road
Middleburg, FL | 32068 | (904) 272-6408 | Clay | private | |
| Rideout Elementary School | PK-6 | 3065 Apalachicola Blvd
Middleburg, FL | 32068 | (904) 291-5430 | Clay | public | Clay County Public Schools |
| Swimming Pen Creek Elementary School | PK-6 | 1630 Woodpecker Lane
Middleburg, FL | 32068 | (904) 278-5707 | Clay | public | Clay County Public Schools |
| Tynes Elementary School | PK-6 | 1550 Tynes Blvd
Middleburg, FL | 32068 | (904) 291-5400 | Clay | public | Clay County Public Schools |
| Wilkinson Junior High School | 7-8 | 5025 County Rd 218 W
Middleburg, FL | 32068 | (904) 589-6100 | Clay | public | Clay County Public Schools |
