He studied at the Collège de Montréal, a Roman Catholic minor seminary in his home town.
While he was attending the Medical School, he met with his childhood friend, Andrew Fernando Holmes.
In 1819, he and Holmes went to Paris to be trained under Philibert Joseph Roux, a surgeon at Hôpital de la Charité, for few weeks.
In September of that year, Roux performed an hour-long operation on Stephenson and his speech became almost normal.
His thesis, "De velosynthesi", written in Latin, explained one of the first successful surgical repairs of cleft of soft palate.