This paper presents the results of the general modelling process for the logistics of medicines distribution within the public health program in Colombia. The model is grounded in verifying the conditions on the current information for the logistics distribution system of the medicines in the six (6) public health programs in Colombia. Verification on the structure and robustness of the created model is developed through an emulation system based on the matrix of real information, and later verified by using a discrete simulation program developed in visual.Net with input and output to Excel. The proposal is tested and validated through GAMS® - General Algebraic Modelling System, with the formulation of three operational scenarios that achieve savings up to 57,44% of the total cost of the public health medicines logistics system.