The presenter, who also fronts BBC Breakfast, joined the football magazine show at the start of the 2009-10 season. His professional broadcasting career started at Hallam FM after he graduated from the University of Sheffield, and he still lives in the area.
His last show will coincide with the end of the current season on Saturday, May 22.
He will continue to present BBC Breakfast and for BBC Sport, including at the Olympics in Tokyo this summer.
Walker said: “It has been an amazing 12 years and I have loved every second of it.
“I am so proud of the job we’ve done, the changes we’ve made and issues we’ve looked at while the football landscape changed immeasurably.
“I’d like to say thank you to the amazing team at Focus who put so much into the show each week and thank you to the audience for tuning in every Saturday.”
Philip Bernie, head of TV at BBC Sport, said: “Dan has been exceptional as presenter of Football Focus for the last 12 years.
“He is a top-class broadcaster who has brought authority, wit and fun to the show, always working so well with such warmth with the guests on the show.
“We are extremely grateful for all he has given to Focus, and will continue to enjoy watching him on the BBC’s sport output as well as the wider BBC.”