Bonilla firmly believed in military education, which is why through Legislative Decree No. 56 of August 26, 1904, issued by the National Constituent Assembly, the Military School of Honduras was created that would be under the auspices of the Ministry of War and the headquarters would be divided between the ground floor of the old Government Palace and another building located in Tocotín , in both in Tegucigalpa. The Director appointed on September 17, 1904 was Lieutenant of Engineers Servando Muñoz.
The applicants to enter the Military School came from the » Cadet School «, Artillery School and from the interior of the country. In the month of May of the year 1904 arrived almost all the young people of the interior, continuing the flow although in smaller volume until the month of December.
In the promotions of the years 1907 and 1912 of School it can be observed that the vast majority of the graduates came from the interior of the country, since only four were natives of Tegucigalpa. By June 1906, the school was being run by Officer Benjamin P. Sánchez, son of General Longino Sánchez.
The government decides to hire an officer abroad to make the academic adjustments at the school. Thus, on July 6, 1906, the government signed a contract with Luis Segundo Oyarzún, Captain of Artillery and born 37 years ago in Santiago de Chile, to direct the Military School.
In March 1907, the cadets had their baptism of fire, defending the government of the founder of the school, General Manuel Bonilla. They entered combat: a group in the Llanos de Lizapa in El Paraíso and another in Namasigue, Choluteca. The chroniclers of the time made reference to the fighting cadets and praised their heroism. The government forces were decimated by the superiority of the weaponry used by the combined forces of Honduras and Nicaragua, which ended up imposing a triumvirate and later Miguel R. Dávila as president of Honduras.
The new government ignored the participation of the Military School in the war campaign and continued to support the center that was already close to graduating its first class. Miguel R. Davila, appointed officers to decisive positions. He bought a batch of rapid-fire machine guns, founded the Army General Staff, and tried to modernize it.
The examinations to which the students were subjected were rigorous in such a way that of the 250 applicants who entered in the year of 1904 only 29 officers graduated in the year 1907 and in the second class of the year 1912 25 officers graduated.
The Military School was closed by General Manuel Bonilla, in his second term of government, on November 30, 1912. Its closure was justified on the grounds that it had deeded, in recent times, from what was prescribed by the Military Ordinance, that exotic practices and customs had been introduced, that discipline and subordination were lacking and that matters of a civil and humanistic nature gravitated very heavily in the pensum of the institution. The government of Miguel R. Dávila was blamed for all this.