Born Fiona Sara Charkham in London, she is the daughter of Jonathan Charkham, an economist and adviser to The Bank of England, and Moira Elizabeth Frances Salmon, daughter of Barnett Alfred and Molly Salmon. Her mother's family, the Salmon family, were co-owners of the J. Lyons & Co. cornerhouse empire. Through the Salmon family, Shackleton is a cousin to Nigella and Dominic Lawson, and George Monbiot.
Shackleton was educated at Benenden School in Kent. She attended Exeter University, graduating with a third class degree in law. Shackleton then trained as a cordon bleu chef, and became an executive caterer for boardrooms before training to be a solicitor. In July 2010, she was awarded an honorary degree from the University of Exeter in the form of an LL.D.
Shackleton qualified as a solicitor in 1980, and by 1986 she had become a partner at Farrer and Co, the firm of solicitors employed by the Royal Family. In the same year Shackleton and other international family lawyers, including Jane Simpson and Raymond Tooth, co-founded the International Academy of Matrimonial Lawyers, an invitation-only organisation which now consists of over 500 of the world's leading family lawyers. Her first high-profile case was that of The Duke and Duchess of York.
Shackleton joined Payne Hicks Beach in 2001 as a partner. Shackleton is reputed to have fallen out of royal favour in the aftermath of the Paul Burrell affair and the suggestions of a cover-up over allegations of a homosexual rape within the royal household put Shackleton, in her own words, "Under pressure for a solution to be reached more speedily than I was able to achieve". She was criticised in the Peat Report on the proceedings.