On 27 December 1858 he was made almoner to the nuns of order of the Sisters of the Infant Jesus at Chauffailles - this experience of apostolic ministry and of spiritual direction moved him to enter the Missions étrangères de Paris seminary aged thirty.
He became a French teacher and took part in the construction of a church dedicated to the Twenty-Six Martyrs of Japan, overlooking the sea - it was designed by Girard and Furet and opened on 19 February 1865.
The imperial repression of Christianity only ended in 1873 and that year Petitjean was allowed back by the Japanese authorities, initially only on the condition that he only give the sacraments to foreign soldiers, sailors and merchants in Japan's ports.
Pius IX sent Petitjean the apostolic letter Dum asperrimam in May 1873 to express his joy at the end of the persecution and the start of a limited degree of tolerance of Christianity by the authorities.
The latter was entrusted to Pierre-Marie Osouf - Petitjean was one of two bishops to consecrate him in 1877 in the chapel of the Missions étrangères on rue de Bac in Paris.
At the time of his death Japan had 30,230 Christians, two bishops, 53 European missionaries (mainly French), three Japanese-born priests (all ordained by Petitjean on 31 December 1882, the first ever in the country), two seminaries with 79 students and 65 schools with 3,331 pupils.