| 1 | The Alice Springs Steiner School (Private) | Alice Springs | 1125 |
| 2 | St Philip's College (Private) | Alice Springs | 1062 |
| 3 | The Essington School Darwin (Private) | Nightcliff | 1046 |
| 5 | Nhulunbuy Christian School (Private) | Nhulunbuy | 1043 |
| 6 | Milkwood Steiner School (Private) | Berrimah | 1038 |
| 11 | Holy Family Primary School (Private) | Karama | 1018 |
| 12 | O'Loughlin Catholic College (Private) | Sanderson | 1017 |
| 14 | Good Shepherd Lutheran College (Private) | Palmerston | 1011 |
| 14 | Palmerston Christian School (Private) | Marlow Lagoon | 1011 |
| 16 | St Paul's Primary School (Private) | Nightcliff | 1008 |
| 18 | St Francis of Assisi School (Private) | Humpty Doo | 1004 |
| 20 | Our Lady of the Sacred Heart College (Private) | Alice Springs | 1000 |
| 21 | Marrara Christian School (Private) | Marrara | 998 |
| 23 | St Andrew Lutheran School (Private) | Leanyer | 990 |
| 27 | Holy Spirit Primary School (Private) | Wanguri | 978 |
| 29 | St Mary's Primary School (Private) | Darwin | 972 |
| 30 | Kormilda College (Private) | Berrimah | 971 |
| 33 | Living Waters Lutheran Primary School (Private) | Alice Springs | 962 |
| 39 | Araluen Christian College (Private) | Alice Springs | 946 |
| 45 | St Joseph's College (Private) | Katherine | 923 |
| 47 | Sacred Heart School (Private) | Palmerston | 915 |
| 61 | St John's College (Private) | Stuart Park | 871 |
| 62 | Northern Territory Christian College (Private) | Marrara | 869 |
| 74 | Nyangatjatjara College (Private) | Yulara | 797 |
| 87 | Yipirinya School (Private) | Alice Springs | 674 |
| 88 | Xavier Community Education Centre (Private) | Bathurst Island | 669 |
| 92 | Woolaning Homeland Christian College (Private) | Woolaning | 611 |
| 103 | Murrupurtiyanuwu Catholic School (Private) | Bathurst Island | 584 |
| 110 | St Francis Xavier School (Private) | Daly River | 554 |
| 113 | Yirara College (Private) | Alice Springs | 515 |
