In Colombia few companies are innovative. This is especially true of small and medium enterprises (SMEs). While this should be a priority for the government because they represent a significant number of companies, unfortunately innovation policies have not been oriented towards these. The aim of this article is to determine the challenges of the Colombian innovation policy regarding SMEs. An investigation was conducted with a qualitative descriptive approach through a documentary review of related regulations and application of semi-structured interviews with experts from the National System of Science, Technology, and Innovation (SNCTI). The research findings show that government initiatives have been implemented, but they were designed in a general fashion; also, though there are instruments, they are largely inaccessible. It is concluded that the challenges encountered can be faced using actions in resources, political will, and strategy.