Masjid Syuhada Yogyakarta has become a witness of Indonesia history of Independence with the spirit and struggle of the Moslems. Masjid Syuhada has candrasengkala (date of establishment in the form of words) and also a commemoration of Independence Proclamation of Republic of Indonesia (17th of August, 1945). It is described in the important parts of the building, such as 17 stairs on the front part, octagonal (8) pillar and four (4) bottom kupel (small cupola) and five (5) top kupel.

The buildings consists of three floors, basement for classroom, with twenty (20) windows as a symbol of 20 characteristics of Allah SWT. There are on second floor which is for praying (shalat) for women, two pillars as a symbol of two good intention of human beings. Whilst on the third floor as the main room for shalat, including Jumatan (Friday praying) at the mihrab, there are five windholes as a symbol of Five Pillars of Islam.

It was on August 17th 1950, the direction (kiblat) was made for the building. On September 23rd 1950 (11 Dzulhijjah 1369) on the second "Hari Raya Qurban", Sri Sultan Hamengku Buwono IX as the Defence Minister of Republic of Indonesia, put the first stone of the establishment of the Masjid. In two years, September 20th 1952, all of the building was done and officially functioned on Hijriyah New Year, 1 Muharram 1372.

Masjid Syuhada Yogyakarta is meant to fulfill the needs of Moslem in general and to give awards to the public of Moslem in Yogyakarta who give support to the society, nation, and country of Indonesia. It is also meant to be a monument for the heroes who was dead (syahid) in struggling the Independence of Indonesia.

The masjid combines several style of architechture, such as in the symbol and the buildings, the cupola takes some shapes of buildings in Persia, India. The main cupola is surrounded by another small cupola on the four directions.

The three floor masjid gives opportunity to the Moslems to have their daily activities on the site. Besides for the center of religion, the existence is expected to be the main activities of the Moslem society. For instance, on the basement, people can function the space for various activities, such as lecture, meetings, etc.