Berikut adalah list museum di Yogyakarta :
| 1 | Living Museum Kotagedhe |
| 2 | Monumen Radio AURI PC-2 |
| 3 | Museum Affandi |
| 4 | Museum Anak “Kolong Tangga” (TBY) |
| 5 | Museum Bahari |
| 6 | Museum Bale Agung (Wates) |
| 7 | Museum Batik Imogiri |
| 8 | Museum Batik Yogyakarta (dekat Hotel Batik) |
| 9 | Museum Benteng Vredeburg |
| 10 | Museum Biologi UGM |
| 11 | Museum Dewantara Kirti Griya (Tamansiswa) |
| 12 | Museum Gembira Loka |
| 13 | Museum Gempa Prof. Sarwidi |
| 14 | Museum Geoteknologi UPN Veteran |
| 15 | Museum Gumuk Pasir |
| 16 | Museum Gunung Merapi |
| 17 | Museum HB IX |
| 18 | Museum Kayu Wanagama |
| 19 | Museum Monumen Kesatuan Pergerakan Wanita Indonesia (KOWANI) |
| 20 | Museum Memorabilia Jenderal Soeharto (Kemusuk) |
| 21 | Museum Monumen Jogja-Kembali |
| 22 | Museum Monumen Pahlawan Pancasila |
| 23 | Museum Monumen Yogya Kembali (Monjali) |
| 24 | Museum Omah UGM (Kotagedhe) |
| 25 | Museum Pangeran Diponegoro |
| 26 | Museum Pendidikan UNY |
| 27 | Museum Pergerakan Wanita Indonesia |
| 28 | Museum Perjuangan Yogyakarta |
| 29 | Museum Romo Mangun |
| 30 | Museum RS Mata Dr. YAP |
| 31 | Museum Sandi |
| 32 | Museum Sasmita Loka Jenderal Sudirman |
| 33 | Museum Sejarah Purbakala Prelet |
| 34 | Museum Sonobudoyo |
| 35 | Museum Sonobudoyo Unit II |
| 36 | Museum Taman Tino Sidin |
| 37 | Museum Tani |
| 38 | Museum Tembi |
| 39 | Museum TNI (Dharma Wiratama) |
| 40 | Museum TNI AU |
| 41 | Museum UGM |
| 42 | Museum Wayang Kekayon |