Brain derived neurotrophic factor (BDNF) is a promising therapeutic candidate for a variety of neurological diseases. However, it is difficult to produce as a recombinant protein. In its native mammalian context, BDNF is first produced as a pro‐protein with subsequent proteolytic removal of the pro‐region to yield mature BDNF protein. Therefore, in an attempt to improve yeast as a host for heterologous BDNF production, the BDNF pro‐region was first evaluated for its effects on BDNF surface display and secretion. Addition of the wild‐type pro‐region to yeast BDNF production constructs improved BDNF folding both as a surface‐displayed and secreted protein in terms of binding its natural receptors TrkB and p75, but titers remained low. Looking to further enhance the chaperone‐like functions provided by the pro‐region, two rounds of directed evolution were performed, yielding mutated pro‐regions that further improved the display and secretion properties of BDNF. Subsequent optimization of the protease recognition site was used to control whether the produced protein was in pro‐ or mature BDNF forms. Taken together, we have demonstrated an effective strategy for improving BDNF compatibility with yeast protein engineering and secretion platforms.