Penney, who took over after Scott Robertson left to coach the All Blacks in 2023, will step down at the end of the current campaign after three seasons in charge.
Penney endured a difficult first year as the Crusaders missed the playoffs in 2024 but guided the Christchurch-based side back to the Super Rugby Pacific title in 2025.
The Crusaders, by far New Zealand's most successful professional rugby team, remain in the hunt for a 14th championship in a full Super Rugby competition with one more round before the playoffs.
"It's been an honour of a lifetime to be the Head Coach of the Crusaders, but the time is right for me to step away from the role after three seasons," Penney said in a Crusaders statement.
Hansen worked as an assistant coach at the Crusaders before joining Robertson's All Blacks staff, but he left the national setup earlier this year after new head coach Dave Rennie took over.
"My family and I are incredibly thankful for this opportunity, and we’re excited to be part of something special,” Hansen said.
"I was born in Christchurch, raised in Lyttelton, and I’m Crusader No. 25. This is my home."