Joseph Chrysostomus Pauer (29 June 1756 – 19 December 1826) was an Austrian prelate of the Catholic Church who served as the bishop of Sankt Pölten from 1824 to his death in 1826.
Pauer previously served as a military vicar of Austria and the titular bishop of Duvno from 1818 to 1824.
Pauer was a Jesuit novice until the Order was abolished in 1773 when he moved to the Barnabites' professed house (Michaelerhaus) near the Church of St. Michael on Michaelerplatz in Vienna.
On 24 April 1815, Pauer was appointed the military vicar of Austria and on 25 May 1818, the titular bishop of Duvno.
His consecration took place on 2 August 1818, with Archbishop Sigismund Anton von Hohenwart of Vienna as the principal consecrator and Titular Bishop Adeodatus Papikian of Ejmiatsin and Titular Bishop Matthias Paul Steindl of Anteapolis as the co-consecrators.