Events from the year 1539 in Ireland.

• Lord: Henry VIII

• The Geraldine League is founded by Manus O'Donnell and Conn O'Neill and begins its invasion of The Pale.^[1][2][3]
• Dissolution of the Monasteries continues including the start of suppression of those within The Pale.^[1] Establishments surrendered include:
  • Ardee Priory Hospital (6 December) and White Friars Priory.
  • Arklow Priory.
  • Athboy Friary.
  • Athy Priory (30 April).
  • Bangor Abbey.
  • Cloncurry Friary (30 April).
  • Clonmines Friary.
  • Dundalk Priory Hospital (23 November).
  • Enniscorthy Abbey and Priory.
  • Fore Abbey (27 November).
  • Graney Abbey, Co. Kildare (7 February).
  • Grey Abbey, Kildare (30 April).
  • White Abbey, Kildare (April).
  • Kells Monastery, Co. Meath.
  • Kilcullen Abbey (by 30 April).
  • Killodry Priory.
  • Knock Abbey, Co. Louth.
  • Lismullin Priory, Co. Meath.
  • Louth Priory (20 November).
  • Mellifont Abbey (23 July).
  • Mullingar Priory (28 November).
  • Naas Priory (26 July).
  • Navan Abbey.
  • Odder Priory, Co. Meath.
  • Portrane Priory.
  • Priory Hospital of St. John the Baptist, Drogheda (26 July).
  • Priory Hospital of St. John the Baptist, Newtown Trim.
  • Rosbercon Abbey (20 June).
  • St. Catherine's Priory, Co. Dublin (25 June).
  • St. Catherine's Priory, Waterford.
  • St. John the Baptist Hospital, Dublin.
  • St. Mary's Abbey, Dublin (28 October).
  • St. Mary's Carmelite Friary, Dublin (3 August).
  • St. Saviour Dominican Friary, Dublin.
  • Skreen Friary.
  • Termonfeckin Abbey.
  • Tintern Abbey (County Wexford) (seized 25 July).
  • Tipperary Friary (7 April).
  • Tristernagh Abbey (by 10 December).
• Lands at Monkstown, County Dublin, granted to Sir John Travers, Master of the Ordnance in Ireland. ^{[citation needed]}

• 26 August – Piers Butler, 8th Earl of Ormonde, Lord Treasurer (b. c.1467)^{[citation needed]}