Kongolo, who has spent the last six months at Huddersfield on loan, has signed a four-year contract at the John Smith's Stadium.
"I'm so happy that we've brought Terence back as a permanent Huddersfield Town player ahead of the 2018-19 Premier League season. His signing is a big statement for this club," said Huddersfield boss David Wagner in a statement posted on the club's website.
"We knew he was a top, top player when we brought him in on loan in January; you don't play for the Netherlands in a World Cup and win the Dutch league with Feyenoord otherwise."
Kongolo made 17 appearances for the Terriers during his loan and was instrumental in their Premier League survival.