Margaret Clitherow was born in around 1552 in York and was the daughter of Jane Middleton and Thomas Middleton, a wax chandler and freeman of York. It is believed that she would have been baptised at the Church of St Martin, where her father served as a churchwarden between 1555 and 1558. At around the age of 18, Margaret married John Clitherow in July 1571. John Clitherow was a widower with two sons and a wealthy butcher who became a freeman in 1560 and elected a chamberlain in 1574.

Following her marriage to John, Margaret moved to the Shambles in York, where she helped her husband with his business. Although we know that Margaret had numerous children, we do not know the exact number, but we know that in addition to her stepsons, she had a son Henry and a daughter named Anne. In 1576, she was pregnant and again in 1581. She was released from prison to give birth, but we don’t know whether these children survived.