Sir Thomas Allen, 1st Baronet (c. 1566 – 7 March 1627) was the eldest son of John Alen (d. 29 September 1616) of St. Wolstan's, near Celbridge, County Kildare and Anne, daughter of Thomas Dillon of Riverstown, County Meath.

He was the grandnephew of John Alan, Lord Chancellor of Ireland, who acquired St Wolstan's on the dissolution of the monasteries.

He was created a baronet, of St Wolstan's in the County of Kildare, in the Baronetage of Ireland on 7 June 1622, for the services rendered by his long-dead great-uncle, Archbishop John Alen, and also a payment to the Crown (baronetcies were largely a money-making device).

His estates passed to the heirs of his brother Nicholas.

Ruins of Donaghcumper Church where Sir Thomas was buried in the Alen family vault He should not be confused with Sir Thomas Allen, 1st Baronet, of Totteridge, Middlesex.