She was born in Halifax, Nova Scotia, to James Affleck, a sea captain, and Catherine Saunders.

She has been described by historians as a high-spirited young woman who resembled Catherine Linton in Emily Brontë's Wuthering Heights.

When he was offered the opportunity to become Minister of Justice in 1885, Annie Thompson encouraged him to leave that bunch of "sere old crows" (her words) on the Nova Scotia bench and get out into a world which would better test and demonstrate his talents.

He left a very small estate, and the Lady Thompson Fund was begun that month as a private subscription for the children.

Friends, including Lady Aberdeen and Senator Frank Smith, aided her in finding housing and establishing herself.