Ewen was born in 1831, the eldest child of Donald MacKillop and Catherine Morrison of old Borve. By 1851 he was working as a farm servant for his  paternal grandmother. Not long afterwards the tenants were cleared from Borve, and Ewen's family was removed to the northern part of Berneray, to Quay, then onto Baile. Ewen had a daughter, Mary Ann, with Effie MacDonald of Scolpaig.