The 23-year-old has agreed a deal that will keep him at the club until the end of 2021.
Thompson was a regular in Yorkshire’s T20 side last summer and also made two appearances in the County Championship.
“I’m hoping to play more first team games and cement my place,” he said.
“I’ve debuted in each format over the last few years, so I know what it’s all about now.
“It’s now about performing consistently for the first team.”
Martyn Moxon, Yorkshire’s director of cricket, commented: “Jordan showed huge potential when he played in both the County Championship games and T20s, so hopefully he will continue to progress and become a regular in all formats over the next couple of years.”