| Name | | Location | Primary display/topic | Annual visitors |
| ANU - Museum of the Jewish People | | Tel Aviv | Jewish history | 220,000 |
| Israel Museum | | Jerusalem | Archaeology, art, sculpture | ~1,000,000 |
| Yad Vashem | | Jerusalem | Holocaust | ~1,000,000 |
| Siebenberg House | | Jerusalem | Archaeology | |
| Heichal Shlomo Jewish Heritage Museum | | Jerusalem | Judaica | |
| Menachem Begin Heritage Center | | Jerusalem | Biographical – Menachem Begin | |
| Friends of Zion Museum | | Jerusalem | Jewish history | |
| Beit Agnon | | Jerusalem | Biographical – Shmuel Yosef Agnon | |
| Museum of Underground Prisoners | | Jerusalem | Jewish resistance in the British Mandate | |
| Bible Lands Museum Jerusalem | | Jerusalem | Biblical history, archaeology | |
| Bloomfield Science Museum | | Jerusalem | Hands-on science and technology | 300,000 |
| Ticho House | | Jerusalem | Paintings by Anna Ticho, Judaica | |
| Tower of David | | Jerusalem | History of Jerusalem | 500,000+ |
| Herzl museum | | Jerusalem | Biographical – Theodor Herzl, history of Zionism | |
| U. Nahon Museum of Italian Jewish Art | | Jerusalem | Italian Jewish art, Italian synagogue | 40,000 |
| Jerusalem Tax Museum | | Jerusalem | Historical documents | |
| Tel Aviv Museum of Art | | Tel Aviv | Modern art, contemporary Israeli art | 1,070,714 |
| Frenkel Frenel Museum | | Safed | Art of Franco-Israeli painter and sculptor, Isaac Frenkel Frenel | |
| Independence Hall | | Tel Aviv | History of Israel | |
| Batei HaOsef | | Formerly Tel Aviv, now being transferred to Latrun | Israel Defense Forces | |
| Bauhaus Museum | | Tel Aviv | White City of Tel Aviv | |
| Bialik House | | Tel Aviv | Hayyim Nahman Bialik | |
| Ben-Gurion House | | Tel Aviv | David Ben-Gurion | |
| Hetzel Museum | | Tel Aviv | Irgun pre-state Jewish underground | |
| Etzel House | | Tel Aviv | Irgun – Operation Hametz | |
| Steinhardt Museum of Natural History | | Tel Aviv | Natural history | |
| Yitzhak Rabin Center | | Tel Aviv | Yitzhak Rabin | 100,000 |
| HerzLilienblum Museum of Banking and Tel Aviv Nostalgia | | Tel Aviv | Banking and old Tel Aviv culture | |
| Lehi Museum – Beit Yair | | Tel Aviv | Lehi | |
| The Olympic Experience | | Tel Aviv | Sports | |
| Nahum Gutman Museum of Art | | Tel Aviv | Art by Nachum Gutman | |
| Farkash Gallery collection | | Tel Aviv | Posters | |
| Ilana Goor Museum | | Tel Aviv | Israeli art and culture | |
| Jaffa Museum | | Tel Aviv | Israeli art and culture, antiquities | |
| Eretz Israel Museum | | Tel Aviv | Archaeology, history of Eretz Yisrael | |
| Beit HaPalmach | | Tel Aviv | Jewish resistance during the British Mandate – Palmach | |
| Haifa Museum | | Haifa | Contemporary Israeli art | |
| Tikotin Museum of Japanese Art | | Haifa | Japanese art | |
| Israel Railway Museum | | Haifa | Transportation – railways | |
| Israeli Clandestine Immigration and Naval Museum | | Haifa | Israel Defense Forces – Sea Corps | |
| Israeli National Maritime Museum | | Haifa | Maritime history | |
| Israel [National Museum of Science, Technology, and Space] | | Haifa | Science and technology, hands-on exhibits | 400,000 |
| Moshe Shteklis Museum of Prehistory | | Haifa | History – prehistory | |
| Hecht Museum | | Haifa | Archaeology, Art | |
| Munio Gitai Weinraub Museum of Architecture | | Haifa | Architecture | |
| Mane-Katz Museum | | Haifa | Art | |
| Arad Bible Museum | | Arad | Archaeology | |
| Arad Doll Museum | | Arad | Comedia del arte figures, handcrafted dolls | |
| Arad Glass Museum | | Arad | Glass sculpture | |
| Arad Museum of Art | | Arad | Art | |
| Beit HaGdudim | | Avihayil | Jewish Legion | |
| Ashdod Museum of Art | | Ashdod | Art | |
| Karin Maman Museum | | Ashdod | Archaeology | |
| Negev Museum of Art | | Beersheba | Art | |
| Biblical Museum of Natural History | | Beit Shemesh | Hands-on animals, Torah, history and science | |
| Ralli Museum | | Caesarea | Art | |
| Ein Harod Museum of Art | | Ein Harod | Art | |
| Sturman Museum | | Ein Harod | Natural history | |
| Janco Dada Museum | | Ein Hod | Art | |
| Wilfrid Israel Museum | | HaZore'a | Art | |
| Air Force Museum">Israeli Air Force">Air Force Museum | | Hatzerim Airbase | Israel Defense Forces – Air Force | |
| Herzliya Museum of Contemporary Art | | Herzliya | Art | |
| Holon Children's Museum | | Holon | Children; visually impaired; hearing impaired | |
| Design Museum Holon | | Holon | Design | |
| Egged Historical Vehicle Museum | | Holon | Transportation – buses | |
| Yad La-Shiryon | | Latrun | Israel Defense Forces – Armor Corps | |
| Mini Israel | | Latrun | Miniature park, architecture | |
| Ghetto Fighters' House | | Lohamei HaGeta'ot | Holocaust and Jewish Resistance | |
| Museum of Prehistory of the Hulah Valley | | Ma'ayan Barukh | Archaeology | |
| Masada Museum | | Masada | History of Masada | |
| International Jewish Sports Hall of Fame | | Netanya | Sports | |
| Petah Tikva Museum of Art | | Petah Tikva | Art | |
| Museum of Israeli Art | | Ramat Gan | Art | |
| Museum of Russian Art | | Ramat Gan | Art | |
| Yehiel Nahari Museum of Far Eastern Art | | Ramat Gan | Art | |
| Yemenite Jewish [Heritage Center and Museum] | | Rehovot | Yemenite Jewish Heritage | |
| Rishon LeZion City Museum | | Rishon LeZion | City | |
| The Arab [Museum of Contemporary Art (Sakhnin)|The Arab Museum of Contemporary Art] | | Sakhnin | Art | |
| Museum for Archaeology and Knowledge of Israel | | Sasa | Archaeology | |
| Qassam Museum | | Sderot | Qassam rockets | |
| German-Speaking Jewry Heritage Museum Tefen | | Tefen Industrial Zone | Jewish history | |
| Umm al-Fahm Art Gallery | | Umm al-Fahm | Art | 40,000 |
| Beit HaTotchan | | Zikhron Ya'akov | Israel Defense Forces – Artillery Corps | |
| | Old Jaffa, Tel Aviv-Yafo | Art, History | |