Aylmer was born at Painstown, Kilcock, County Kildare, on 29 August 1786.
His father, also called Charles Aylmer, attended the Catholic Convention in 1792.
He became rector of Clongowes Wood College, in Ireland, in 1817, was professed of the four vows 16 January 1820, and lived in Dublin from about 1821 until his death on 4 July 1847.
He was superior of the Dublin Residence in 1816, 1822, and 1829 (when the first stone of the church in Gardiner Street was laid), and again in 1841.
Father Aylmer promoted in Dublin a society for the printing of Catholic books.