In the past few decades there has been an increasing demand of biopharmaceutical proteins in the market. Several types of cell factories are applied to produce different pharmaceutical proteins. However, manufacturers prefer to use a few favorable biological platforms to undertake the production tasks with low cost, high productivity and proper post-translational modifications. The yeast Saccharomyces cerevisiae is one of these preferred cell factories as it meets many of the requirements. There are several reports on improvement of recombinant protein production by S. cerevisiae through rational engineering of different stages of the protein secretion pathway. However, recent developments of new technologies like systems biology and synthetic biology open new doors to design S. cerevisiae as an ideal production platform.