Aeneas Chisholm (1759–1818) was a Roman Catholic bishop who served as the Vicar Apostolic of the Highland District, Scotland.

In 1786 he was nominated prefect of studies in the Scots College, Douai.

He was appointed the Coadjutor Vicar Apostolic of Highland District and Titular Bishop of Diocaesarea in Palaestina by the Holy See on 11 May 1804.

The principal consecrator was Bishop Alexander Cameron, Vicar Apostolic of the Lowland District.

Following the death of his brother Bishop John Chisholm on 8 July 1814, Aeneas automatically succeeded as the Vicar Apostolic of Highland District.