| Name | Location | Type | Summary |
| Afro-Antillean Museum | Panama City | Culture | , history and culture of the West Indian workers for the building of the Panama Canal |
| Biomuseo | Panama City | Natural history | |
| Belisario Porras Museum | Las Tablas | Biographical | , life of politician Belisario Porras Barahona |
| Bolivar Museum | Panama City | History | |
| National Bank of Panama House Museum | Panama City | Numismatic | ,, operated by National Bank of Panama. |
| El Pausilipo Museum | Las Tablas | History | |
| Manuel F. Zarate Museum | Guararé | Culture | , folklore and clothing |
| Marine Exhibition Center of Punta Culebra | Panama City | Natural history | Nature center with aquariums |
| Stella Sierra Regional Museum of Aguadulce | Aguadulce | History | , formerly the Salt and Sugar Museum, local history, salt and sugar industries |
| Museum of Contemporary Art | Panama City | Art | |
| Museum of History | Panama City | History | |
| Nationality Museum | La Villa de Los Santos | | |
| Natural Sciences Museum | Panama City | Natural history | , stuffed and mounted animals, rocks and minerals. |
| José de Obaldía Museum of History and Art | David | History and Art | Closed |
| Panama Canal Museum | Panama City | History | History of the construction of the Panama Canal |
| Penonomé Museum | Penonomé | History and Culture | |
| Portobelo Royal Customs House Museum | Portobelo | History | |
| Reina Torres de Araúz Anthropological Museum | Panama City | Anthropology | , archaeological and ethnographic artifacts |
| Religious Art Museum | Panama City | Art | |
| Ricardo J. Alfaro Museum | Panama City | Biographical | |