| Name | Location | Primary display/topic | Annual visitors | | Israel Museum | Jerusalem (Givat Ram) | Archaeology, art, sculpture | 827,254 (2012)[1] |
| Yad Vashem | Jerusalem (Mount Herzl) | Holocaust | ~1,000,000 |
| Rockefeller Museum | Jerusalem (East Jerusalem) | Archaeology |
| Siebenberg House | Jerusalem (Old City) | Archaeology |
| L. A. Mayer Institute for Islamic Art | Jerusalem (Katamon) | Islamic art, antique clocks & watches |
| Gush Katif Museum | Jerusalem (Nachlaot) | History (Gush Katif) |
| Heichal Shlomo Jewish Heritage Museum | Jerusalem (King George Street) | Judaica |
| Menachem Begin Heritage Center | Jerusalem | Biographical – Menachem Begin |
| Friends of Zion Museum | Jerusalem | Jewish history |
| Beit Agnon | Jerusalem (Talpiot) | Biographical – Shmuel Yosef Agnon |
| Museum of Underground Prisoners | Jerusalem (Morasha) | Jewish resistance in the British Mandate |
| Bible Lands Museum Jerusalem | Jerusalem (Givat Ram) | Biblical history, archaeology |
| Bloomfield Science Museum | Jerusalem (Givat Ram) | Hands-on science and technology |
| Ticho House | Jerusalem | Paintings by Anna Ticho, Judaica |
| Tower of David | Jerusalem (Old City) | History of Jerusalem | 450,000 (2017)[2] |
| Herzl museum | Jerusalem (Mount Herzl) | Biographical – Theodor Herzl, history of Zionism |
| U. Nahon Museum of Italian Jewish Art | Jerusalem | Italian Jewish art, Italian synagogue |
| Jerusalem Tax Museum[3] | Jerusalem (Jaffa Road) | Historical documents |
| Tel Aviv Museum of Art | Tel Aviv | Modern art, contemporary Israeli art | 750,000 (2012)[1] |
| Independence Hall | Tel Aviv | History of Israel (independence) |
| Batei HaOsef | Tel Aviv | Israel Defense Forces |
| Etzel Museum | Tel Aviv | Irgun pre-state Jewish underground |
| 5708 Etzel Museum – Beit Gidi | Tel Aviv | Irgun – Operation Hametz |
| Herzlilienblum Museum of Banking and Tel Aviv Nostalgia[4] | Tel Aviv | Banking and old Tel Aviv culture |
| Lehi Museum – Beit Yair | Tel Aviv (Florentin) | Lehi |
| The Olympic Experience | Tel Aviv (Hadar Yosef) | Sports |
| Nachum Gutman Museum | Tel Aviv (Neve Tzedek) | Art by Nachum Gutman |
| Farkash Gallery collection | Tel Aviv (Old Jaffa) | Posters |
| Ilana Goor Museum | Tel Aviv (Old Jaffa) | Israeli art and culture |
| Jaffa Museum | Tel Aviv (Old Jaffa) | Israeli art and culture, antiquities |
| Eretz Israel Museum | Tel Aviv (Ramat Aviv) | Archaeology, history of Eretz Yisrael |
| The Museum of The Jewish People at Beit Hatfutsot | Tel Aviv (Ramat Aviv) | A pluralistic and diverse experience of the Jewish people |
| Beit HaPalmach | Tel Aviv (Ramat 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 |
| 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[5] |
| 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 |
| Janco Dada Museum | Ein Hod | Israeli art |
| Israeli Air Force Museum | Hatzerim Airbase | Israel Defense Forces – Air Force |
| Herzliya Museum of Contemporary Art[6] | Herzliya | Contemporary Israeli 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 |
| Harry Oppenheimer Diamond Museum | Ramat Gan | Diamonds |
| Museum of Israeli Art | Ramat Gan | Art (Israeli) |
| Museum of Russian Art | Ramat Gan | Art (Russian) |
| Yehiel Nahari Museum of Far Eastern Art | Ramat Gan | Art (Far Eastern) |
| Yemenite Jewish Heritage Center and Museum | Rehovot | Yemenite Jewish Heritage |
| Rishon LeZion City Museum | Rishon LeZion | City |
| The Arab Museum of Contemporary Art | Sakhnin | Art (Contemporary Arab, Israeli and Mediterranean 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[7][8] | Umm al-Fahm | Art (Arab) |
| Beit HaTotchan | Zikhron Ya'akov | Israel Defense Forces – Artillery Corps |
| Wilfrid Israel Museum | Kibbutz HaZore'a | Asian art |
|
| Mishkan Le'Omanut Ein Harod | Kibbutz Ein Harod | Israeli art |
1. ^1 http://www.theartnewspaper.com/attfig/attfig12.pdf {{webarchive |url=https://web.archive.org/web/20150102172933/http://www.theartnewspaper.com/attfig/attfig12.pdf |date=January 2, 2015 }}
2. ^{{cite news|url=https://www.haaretz.com/israel-news/40m-expansion-renovation-planned-for-history-of-jerusalem-museum-1.6091820|title=$40 Million Expansion-renovation Planned for Jerusalem’s Tower of David Museum|author=Riba, Naama|work=Haaretz|date=May 15, 2018|accessdate=June 4, 2018}}
3. ^{{cite news| url=http://www.haaretz.com/israel-s-past-seen-anew-as-jerusalem-s-historic-custom-house-reopens.premium-1.431161 | title=Israel's past seen anew, as Jerusalem's historic Custom House reopens | publisher=Haaretz }}
4. ^{{cite news| url=http://www.jpost.com/Local-Israel/Tel-Aviv-And-Center/Feel-the-heartbeat-of-Old-Tel-Aviv | title=Feel the Heartbeat of Old Tel Aviv | newspaper=Jerusalem Post }}
5. ^{{cite web|url=http://www.artportal.co.il/?CategoryID=418&ArticleID=362 |title=Arad Doll Museum |website=ArtPortal.co.il |location=Israel |deadurl=yes |archiveurl=https://web.archive.org/web/20160306133158/http://artportal.co.il/?articleid=362&categoryid=418 |archivedate=2016-03-06 |df= }}
6. ^{{cite web| url=https://www.jewishvirtuallibrary.org/jsource/Society_%26_Culture/Herzliyamuse.html | title=Herzliya Museum of Contemporary Art | website=JewishVirtualLibrary.org }}
7. ^{{cite news| url=https://www.theguardian.com/world/view-from-jerusalem-with-harriet-sherwood/2011/mar/10/new-museum-umm-al-fahm | title=Israel to get first museum of Arab art and culture | newspaper=The Guardian | location=UK }}
8. ^{{cite web | url=http://www.haaretz.com/israel-news/culture/.premium-1.662641 | title=When Is an Arab Museum Not an Arab Museum? | publisher=Haaretz | accessdate=22 August 2016}}