Paul, 38, will join 'Well from the Scottish FA at the end of the current women's season.
"I'm delighted to be given this opportunity," said Brownlie, who will officially take over in early June. "The challenge is going to be exciting.
"First and foremost, it's about getting Motherwell FC in the best position possible through my experience of the game, looking at how we can go and compete at the right end of the league.
"In terms of the academy, we want to get it out the best level possible, and that remit falls with me.
"We want Motherwell to be the place girls want to come to develop in Scotland. We need only to look at the success the boys have had and ask if we can mirror that success by putting in the work to make it one of the best academies in Scotland."
Paul, who will also undertake the role of head of women and girl's performance with Motherwell Women, was a senior member of Celtic's women's academy for seven years.
The Scottish FA then headhunted him to be their high performance football manager, which involved the planning, coordinating, delivering and evaluating all aspects of the National Performance Centre's performance programme, based at Heriot-Watt University, in conjunction with the Scottish FA’s national coach for girl's and women’s football.
In addition to that, Paul was also involved in the youth and senior women's international teams, including the under 15s, 16s, 17s and the A squad. He also coached in the Motherwell elite men's academy at Braidhurst between 2018 and 2020.
"We ran what I believe to be a very extensive and robust recruitment process through Sport Careers Agency, which has concluded with Paul's appointment," Motherwell chief executive Alan Burrows said.
"I am extremely thankful to everyone who applied and took part in that, which was both enlightening and exciting.
"In Paul, I believe I have someone who can not only lead our senior team in SWPL1 but also help us shape what we hope will be one of the best girls academies in the country.
"My aim has always been to have someone to really drive this side of the club forward. To give ownership to someone to really grow what we believe is an area of huge potential.
"We believe Paul not only has the ability and experience necessary to do that but the determination for it too. I am really looking forward to working with him."
After the shock departure of Eddie Wolecki Black as Motherwell Women’s gaffer in April, Stewart Hall and Willie Kinniburgh were appointed as interim managers until the end of this season.