In 1936, under the government of Colonel Rafael Franco, the Ministry of Public Health was created by the promulgation of Decree Law No. 2,000/36 of June 15, 1936; while, by Decree Law No. 2,001/36, the organization and functions of the new Secretariat of State were established.

Prior to 1936, all health services were provided and administered by the Ministry of the Interior, but the health consequences of the Chaco War (1932-1935) on the Paraguayan population led the Government to believe it was appropriate to create a Ministry of Public Health.

At that time, one of the main objectives of the State portfolio was to provide medical assistance to the wounded and mutilated in the Chaco conflict, and to effectively control the treatment and transmission of diseases, such as malaria, dysentery and typhoid, which migrated to the Western Region once the Chaco War ended, with the return of the combatants to their homes.

It was not until 1998 that Decree Law No. 2,001/36 was repealed with the promulgation of Decree No. 21,376/98, which established the new functional organization of the Ministry of Public Health and Social Welfare. This official document was signed by the then President of the Republic, Juan Carlos Wasmosy, and promoted by Minister Andrés Vidovich Morales, in accordance, according to its first article, with the relevant precepts of the National Constitution and the development of the National Health System.

In this regulation, now in force, special emphasis was placed on the guiding role of human and environmental health, and social well-being, which was to be fulfilled by the Ministry of Public Health, which, from that moment on, began a period of reforms and modernizations, mainly legislative.