A new catalytic asymmetric desymmetrization reaction for the synthesis of enantioenriched derivatives of 2‐azabicyclo[3.3.1]nonane, a key motif common to many alkaloids, has been developed. Employing a cyclohexanediamine‐derived primary amine organocatalyst, a range of prochiral cyclohexanone derivatives possessing an α,β‐unsaturated ester moiety linked to the 4‐position afforded the bicyclic products, which possess three stereogenic centers, as single diastereoisomers in high enantioselectivity (83–99 % ee) and in good yields (60–90 %). Calculations revealed that stepwise CC bond formation and proton transfer via a chair‐shaped transition state dictate the exclusive endo selectivity and enabled the development of a highly enantioselective primary amine catalyst.