A significant aspect of hydroboration–oxidation is the regio- and stereochemical outcome of the reaction.

Hydroboration proceeds in a concerted fashion with the attack of borane on the π bond, giving a cyclic four-centered transition state. The –BH₂ group is bonded to the less substituted carbon and –H to the more substituted carbon. The concerted nature requires the simultaneous addition of –H and –BH₂ across the same face of the alkene giving syn stereochemistry.

The observed preference in regioselectivity can be explained on the basis of steric and electronic factors.

In the transition state, the larger part of the reagent (–BH₂) is bonded to the less substituted carbon, thereby minimizing the steric tension. This results in a less crowded low-energy transition state, which is more stable than Markovnikov's transition state.

Further, the addition of borane can result in a partial positive charge on either of the two carbons. However, a partial positive charge on the more substituted carbon is highly favorable, as it gives a more stable transition state. Hence, in order to achieve this, –BH₂ must be placed at the less substituted carbon resulting in an anti-Markovnikov orientation.

The second part of the reaction is the oxidation of the product obtained from hydroboration.

The migration of the alkyl group in this mechanism occurs with retention of configuration as it transfers with the electron pairs without reconstructing the tetrahedral geometry of the migrating carbon.

Since the reaction is stereospecific, it is essential to recognize the number of chiral centers formed. If one chiral center is formed, both enantiomers are obtained, as syn addition can occur from either face of the alkene with equal probability. However, if two chiral centers are formed, the syn addition dictates which pair of enantiomers is predominantly obtained.