The defender played 36 times for the Cottagers last term as they reached the Sky Bet Championship play-offs.
Vice chairman Tony Khan told the club’s official website: “It’s a pleasure to welcome Tomas back to the club.
“We appreciate Tomas so much after the way that he battled for us last season, demonstrating not only tremendous skill but also great heart and determination.
“We’re very excited to have him here again as one of us as we prepare for our next battle, and what we hope will be a great season.”
The 24-year-old has won seven caps for the Czech Republic and earned promotion to the Premier League while on loan at Middlesbrough in 2016.
He joined Chelsea in 2010 from Sigma Olomouc and has played four times for the Blues having also spent two years on loan at Vitesse Arnhem.