Justin Chabot has resigned from his position as Northwestern’s director of football operations and is going to work as a Midwest regional scout for the San Francisco 49ers.

Although Chabot agreed to a contract and is listed as a staff member on the 49ers’ Web site, his contract has not yet been finalized. His departure will end a five-year stint on NU’s staff.

Chabot said the decision wasn’t easy, but ultimately he couldn’t pass on the chance to work for San Francisco.

“Of course it’s difficult to leave,” Chabot said. “I spent five years as a player and another five on the staff. This is a place that has been very good to me. But the opportunities that the 49ers provided are great.”

Chabot declined to say when he made the decision, but NU announced his intentions Wednesday. His resignation will be effective June 1.

An NU spokesman said football coach Randy Walker is expected to name a successor in June.

Working in the Midwest will allow Chabot to continue living in the Chicago area, where he has spent most of his adult life.

“I’m excited to have the opportunity to continue to work with Northwestern,” he said.

Chabot declined to comment further until the 49ers approve his contract. He expects it to be approved early next week.

Chabot started 41 games on NU’s offensive line from 1993 to 1996. Like current NU linebackers coach Pat Fitzgerald, Chabot started on the Wildcats’ Rose Bowl team in 1995 and captained the 1996 team that went to the Citrus Bowl.

He also was voted first team all-Big Ten in 1996 by both the media and coaches.

After graduating from NU with a degree in sociology, Chabot spent a brief period playing professional football. In 1997 he played for both the Pittsburgh Steelers and the New York Giants.

He spent a year working at a benefits consulting firm in Chicago before returning to work for NU. He became director of football operations in 1999.

Chabot’s job was to handle off-the-field issues such as travel arrangements.

Chabot is the second member of the NU football organization who has made an agreement with the 49ers recently. Former running back Jason Wright signed with San Francisco just after the NFL draft in April.

Chabot said the two transactions are completely unrelated.

“It was just the right step for me professionally,” he said.