Born in Bradford, West Yorkshire in 1989, Bairstow displayed his early talent when he was chosen as the inaugural winner of the Young Wisden Schools Cricketer of the Year award. This was for the form he showed in 2007 for St Peter's School, York when he scored 654 runs.

He is the second son of former Yorkshire and England wicket-keeper David Bairstow and the half-brother of former Derbyshire player Andrew Bairstow. He is often referred to as 'Young Jonny Bairstow', 'Yorkshire's Jonny Bairstow' or 'YJB' by fans.

During the 2008 season, he played second XI cricket for Yorkshire, in six championship matches he scored 308 runs at an average of 61.60. He was called up to the first-team squad for the final County Championship match of the season against Sussex but failed to make the starting eleven. At the end of the season he signed a two-year professional contract.

Bairstow began the 2009 season playing second XI cricket but after scoring 202 not out against Leicestershire seconds, he was called up into the first-team match with Somerset when Michael Vaughan was ruled out through injury. On his first-class debut he scored 28 before being bowled by Michael Munday. In the second innings he top scored with an unbeaten 82. In Somerset's second innings he took over the gloves from an injured Gerard Brophy and took four catches.

Bairstow was a regular in the Yorkshire team in 2010, playing 16 first-class matches and scoring 918 runs. He averaged more than 40 for a second successive season, but could not convert any of his eight fifties into a maiden century. His performances led to selection for the England Performance Programme squad to tour Australia in 2010/11.

He took the gloves for the 2011 season and started well with the bat by scoring his first 100 against Nottinghamshire in May, finishing on 205. He was the only Yorkshire batsman to score over 1000 runs in the season and on the back of his strong performances was called up to the England one day squad at the end of the season.