Herein, we report a novel cobalt-catalyzed stereo divergent transfer hydrogenation of alkynes to Z- and E-alkenes. Effective selectivity control is achieved based on a rational catalyst design. Moreover, this mild system allows for the transfer hydrogenation of alkynes bearing a wide range of functional groups in good yields using catalyst loadings as low as 0.2 mol %. The general applicability of this procedure is highlighted by the synthesis of more than 50 alkenes with good chemo- and stereoselectivity. A preliminary mechanistic study revealed that E-alkene product was generated via sequential alkyne hydrogenation to give Z-alkene intermediate, followed by a Z to E alkene isomerization process.