| Astoria Lutheran School | Astoria | PreK-8 | 60 | 6 | Evangelical Lutheran Church in America |
| El Ber Islamic School | Astoria | PreK-2 | 28 | 9.3 | Islamic |
| Immaculate Conception Catholic Academy in Astoria | Astoria | PreK-8 | 120 | 7.7 | Roman Catholic |
| Les Enfants Montessori School | Astoria | K-3 | 42 | 4.2 | Nonsectarian |
| St. Demetrios School | Astoria | K-12 | 429 | 6.9 | Greek Orthodox |
| St. Francis of Assisi Catholic Academy | Astoria | PreK-8 | 230 | 12.8 | Roman Catholic |
| St. Irene Chrysovalantou | Astoria | K-8 | 60 | 31.6 | Greek Orthodox |
| St. John's Preparatory School | Astoria | 9-12 | 614 | 19.2 | Roman Catholic |
| Lutheran Church Schools of Flushing & Bayside | Bayside | PreK-8 | 33 | 8.5 | Lutheran Church (Missouri Synod) |
| Sacred Heart School | Bayside | PreK-8 | 153 | 9.7 | Roman Catholic |
| St. Francis de Sales Catholic Academy | Belle Harbor | PreK-8 | 563 | 19.8 | Roman Catholic |
| St. Gregory the Catholic Academy | Bellerose | K-8 | 168 | 13.3 | Roman Catholic |
| Yeshiva Har Torah | Bellerose | PreK-8 | 795 | 7.6 | Jewish |
| Archbishop Molloy High School | Briarwood | 9-12 | 1,601 | 13.6 | Roman Catholic |
| Theresa Paplin School | Briarwood | 4-12 | 37 | 4.1 | Nonsectarian |
| Congregation Ymh | Brooklyn | 9-11 | 87 | 5.8 | Jewish, all-boys |
| Midrash L'man Achai | Brooklyn | 8-11 | 35 | 7 | Jewish, all-boys |
| Stepping Stone of Southeastern Queen School | Cambria Heights | PreK-K | 12 | 4 | Nonsectarian |
| Word Christian Academy | Cambria Heights | K-8 | 10 | 3.3 | Christian (nondenominational) |
| Our Lady of Sorrows Catholic Academy | Corona | K-8 | 225 | 25 | Roman Catholic |
| St. Leo Catholic Academy | Corona | PreK-8 | 148 | 12 | Roman Catholic |
| Divine Wisdom Catholic Academy | Douglaston | PreK-8 | 290 | 11.9 | Roman Catholic |
| Lexington School for the Deaf | East Elmhurst | PreK-12 | 198 | 5 | Nonsectarian |
| Our Lady of Fatima School | East Elmhurst | PreK-8 | 205 | 16.3 | Roman Catholic |
| Cathedral Preparatory School and Seminary | Elmhurst | 9-12 | 160 | 10.7 | Roman Catholic, all-boys |
| St. Adalbert Catholic Academy | Elmhurst | K-8 | 158 | 13.7 | Roman Catholic |
| St. Bartholomew Catholic Academy | Elmhurst | K-8 | 164 | 15 | Roman Catholic |
| Bais Yaakov Ateres Miriam | Far Rockaway | PreK-10 | 276 | 10.8 | Jewish, all-girls |
| Bnos Bais Yaakov / Tichon Meir Moshe | Far Rockaway | 9-12 | 393 | 17.6 | Jewish, all-girls |
| Bnos Bais Yaakov-Far Rockaway | Far Rockaway | PreK-12 | 1,331 | 6.3 | Jewish, all-girls |
| Darchei Torah | Far Rockaway | PreK-12 | 2,165 | 7.3 | Jewish, all-boys |
| Tag High School | Far Rockaway | 9-12 | 448 | 6.2 | Jewish, all-girls |
| Torah Academy for Girls | Far Rockaway | PreK-12 | 1,695 | 8.2 | Jewish, all-girls |
| World Harvest Deliverance Ctr Christian Academy | Far Rockaway | PreK-8 | 8 | 2.7 | Christian (nondenominational) |
| Yeshiva Darchei Torah | Far Rockaway | K-12 | 2,092 | 5 | Jewish, all-boys |
| Yeshiva of Far Rockaway | Far Rockaway | 9-12 | 108 | 8.1 | Jewish, all-boys |
| Flushing Christian School | Flushing | K-8 | 139 | 11.3 | Christian (nondenominational) |
| Lowell High School | Flushing | 9-12 | 153 | 7 | Nonsectarian |
| Mesivta Chofetz Chaim | Flushing | 9-12 | 116 | 11 | Jewish, all-boys |
| Mesivta Yesodei Yeshurun | Flushing | 9-12 | 159 | 10.2 | Jewish |
| Muslim Center Junior High School | Flushing | PreK-8 | 160 | 11.9 | Islamic |
| Our Lady of Mercy Catholic Academy | Flushing | PreK-8 | 247 | 18.6 | Roman Catholic |
| Promise Christian Academy | Flushing | PreK-8 | 130 | 10.8 | Assembly of God |
| Shevach High School | Flushing | 9-12 | 245 | 7.8 | Jewish, all-girls |
| Shield Institute of Flushing | Flushing | PreK | 33 | 6.6 | Nonsectarian |
| Solomon Schechter School of Queens | Flushing | PreK-8 | 396 | 15.2 | Jewish |
| St. Andrew Avellino Catholic Academy | Flushing | PreK-8 | 185 | 15.4 | Roman Catholic |
| St. Mel Catholic Academy | Flushing | PreK-6 | 124 | 13.2 | Roman Catholic |
| The Learning Tree STEM-Arts School | Flushing | 1-8 | 73 | 6.1 | Nonsectarian |
| The Windsor School | Flushing | 7-12 | 100 | 12.5 | Nonsectarian |
| William Spyropoulos Greek-American Day School | Flushing | K-8 | 374 | 12.9 | Greek Orthodox |
| Yeshiva Ketana of Queens | Flushing | K-8 | 417 | 18.3 | Jewish, all-boys |
| Yeshiva of Central Queens | Flushing | PreK-8 | 848 | 6.6 | Jewish |
| Bnos Malka Academy | Forest Hills | PreK-8 | 390 | 13.3 | Jewish, all-girls |
| Ezra Academy | Forest Hills | 9-12 | 98 | 4.9 | Jewish |
| Forest Hills Montessori School | Forest Hills | PreK-6 | 41 | 5.3 | Nonsectarian |
| Our Lady Queen of Martyrs Catholic Academy | Forest Hills | K-8 | 271 | 14.8 | Roman Catholic |
| Shaarei Zion Ohel Bracha Institution-Girlsdivision | Forest Hills | PreK-11 | 240 | 8.2 | Jewish, all-girls |
| The Kew-Forest School | Forest Hills | PreK-12 | 167 | 5.6 | Nonsectarian |
| Yeshivat Shaarei Tzion-Boys | Forest Hills | PreK-12 | 356 | 14.6 | Jewish, all-boys |
| Hadar Bet Yaakov | Fresh Meadows | 9-12 | 50 | 3.6 | Jewish, all-girls |
| Holy Family Catholic Academy | Fresh Meadows | PreK-8 | 136 | 11.3 | Roman Catholic |
| Jewish Institute of Queens-Boys High School | Fresh Meadows | 7-12 | 81 | 4.4 | Jewish, all-boys |
| St. Francis Prep | Fresh Meadows | 9-12 | 2,480 | 20.5 | Roman Catholic |
| Sacred Heart Catholic Academy | Glendale | PreK-8 | 228 | 17.4 | Roman Catholic |
| The Wellspring Schools | Hollis | PreK-12 | 301 | 8.3 | Islamic |
| St. Helen Catholic Academy | Howard Beach | PreK-8 | 333 | 13.4 | Roman Catholic |
| Garden School | Jackson Heights | PreK-12 | 232 | 6.3 | Nonsectarian |
| St. Joan of Arc Elementary School | Jackson Heights | PreK-8 | 173 | 14 | Roman Catholic |
| Al-Iman School | Jamaica | PreK-9 | 39 | 3.5 | Islamic |
| Allen Christian School | Jamaica | PreK-1 | 16 | 5.3 | African Methodist Episcopal |
| Immaculate Conception Catholic Academy | Jamaica | PreK-8 | 217 | 14 | Roman Catholic |
| Queens Early Childhood Center | Jamaica | Ungraded | 16 | 5.3 | Nonsectarian |
| Rising Stars Islamic School | Jamaica | PreK-5 | 105 | 13.1 | Islamic |
| St. Nicholas of Tolentine Catholic Academy | Jamaica | PreK-8 | 231 | 18.8 | Roman Catholic |
| St. Nicholas-Tolentine | Jamaica | PreK-8 | 232 | 17.7 | Roman Catholic |
| Summit School | Jamaica | 9-12 | 151 | 6.4 | Nonsectarian |
| The Mary Louis Academy | Jamaica | 9-12 | 427 | 10.8 | Roman Catholic, all-girls |
| Yeshiva Tifereth Moshe | Kew Gardens | K-8 | 442 | 8 | Jewish, all-boys |
| Linden SDA School | Laurelton | K-8 | 134 | 8.9 | Seventh-Day Adventist |
| Linden Seventh-Day Adventist School | Laurelton | 1-8 | 117 | 6 | Seventh-Day Adventist |
| St. Joseph Catholic Academy | Long Island City | PreK-8 | 272 | 13.3 | Roman Catholic |
| Martin Luther School | Maspeth | 6-12 | 187 | 8 | Lutheran Church (Missouri Synod) |
| St. Stanislaus Kostka Catholic Academy of Queens | Maspeth | PreK-8 | 254 | 16.4 | Roman Catholic |
| Christ the King High School | Middle Village | 9-12 | 604 | 15.5 | Roman Catholic |
| Our Lady of Hope Catholic Academy | Middle Village | PreK-8 | 409 | 18.8 | Roman Catholic |
| St. Margaret Catholic Academy | Middle Village | PreK-8 | 187 | 16.5 | Roman Catholic |
| Holy Martyrs Armenian Day School | Oakland Gardens | PreK-6 | 53 | 17.1 | Nonsectarian |
| Yeshiva Primary & Junior High School | Oakland Gardens | 1-8 | 74 | 6.8 | Jewish |
| Divine Mercy Catholic Academy | Ozone Park | PreK-8 | 183 | 16.9 | Roman Catholic |
| The Nurturing Center and Academy | Queens Village | PreK-4 | 40 | 8 | Nonsectarian |
| Ss Joachim & Anne School | Queens Village | PreK-8 | 204 | 16.6 | Roman Catholic |
| Resurrection Ascension Catholic Academy | Rego Park | PreK-8 | 172 | 13.8 | Roman Catholic |
| Holy Child Jesus Catholic Academy | Richmond Hill | PreK-8 | 303 | 13.2 | Roman Catholic |
| Shaar Hatorah High School | Richmond Hill | 9-12 | 125 | 21.6 | Jewish, all-boys |
| Tiegerman High School | Richmond Hill | 9-12 | 132 | 7.3 | Nonsectarian |
| Yeshivat Ohr Haiim | Richmond Hill | 3-6 | 63 | 25.2 | Jewish, all-girls |
| Notre Dame Catholic Academy | Ridgewood | PreK-8 | 186 | 18.1 | Roman Catholic |
| St. Rose of Lima Catholic Academy | Rockaway Beach | PreK-8 | 189 | 18.9 | Roman Catholic |
| Yeshiva Mercaz Hatorah of Belle Harbor | Rockaway Park | 9-12 | 37 | 2.7 | Jewish, all-boys |
| Christ Lutheran School | Rosedale | 1-8 | 9 | 3.9 | Lutheran |
| St. Clare Catholic Academy | Rosedale | PreK-8 | 163 | 15.8 | Roman Catholic |
| Al-Ihsan Academy | South Ozone Park | PreK-12 | 484 | 11.8 | Islamic |
| Our Lady of Perpetual Help Catholic Academy | South Ozone Park | PreK-8 | 269 | 17 | Roman Catholic |
| Mesivta Shaarei Pruzdor | Valley Stream | 9-12 | 26 | 3.5 | Jewish, all-boys |
| Circle Academy | Whitestone | PreK-8 | 84 | 12 | Nonsectarian |
| St. Lukes School | Whitestone | PreK-8 | 313 | 13.7 | Roman Catholic |
| The Lowell School | Whitestone | 3-8 | 91 | 7 | Nonsectarian |
| Whitestone Academy | Whitestone | 7-12 | 76 | 6.3 | Nonsectarian |
| St. Thomas the Apostle Catholic Academy | Woodhaven | PreK-8 | 120 | 8.6 | Roman Catholic |
| Jackson Heights School SDA | Woodside | K-8 | 35 | 5.8 | Seventh-Day Adventist |
| Razi School | Woodside | PreK-12 | 164 | 9.4 | Islamic |
| St. Sebastian Catholic Academy | Woodside | K-8 | 249 | 18 | Roman Catholic |
| Tiegerman School at Woodside | Woodside | PreK-11 | 58 | 4.8 | Nonsectarian |