Prodromou previously worked for McLaren between 1991 and 2006 before leaving to join Red Bull, where he was a key member of Adrian Newey's technical team.
"I'm delighted to welcome Peter back to McLaren," chief operating officer Jonathan Neale told the team's website. "We're steadily putting everything in place to ensure that McLaren can once again return to its race- and world championship-winning ways.
"We're under no illusions that we're yet there, but Peter's appointment is a very significant one, and is also a very public reminder that we're adding strength in depth to our organisation all the time."
Prodromou said he is determined to contribute to a new and prosperous era at McLaren, who will move from Mercedes to Honda power units for next season.
"It's fantastic to return to McLaren, and to see a mixture of faces old and new," he commented. "Of course, I have first-hand experience of just what a passionate, focused and capable race team exists within these walls, and I've already seen the enthusiasm and positivity that exists to return McLaren to world championship-winning glory."
McLaren's racing director Eric Boullier added: "Peter has proved beyond doubt that he's one of the most capable and intelligent engineers in Formula One.
"He joins us at an auspicious time; we've spent much of 2014 working to develop and organise our design department, and his arrival neatly coincides with the conclusion of that restructuring. Everyone at McLaren is looking forward to the contribution he'll make as we push ahead with our ambitious plans for the future."