The 35-year-old, who gave birth to son Ethan at the end of October last year, had hoped to return for the Commonwealth Games in Glasgow, but has now opted to hang up her spikes.
McConnell said in a statement: "When I fell pregnant with Ethan I made the decision to continue with training through and post pregnancy and see where that took me. I have now reached the decision that my career as a professional athlete has come to an end.
"I was always a working athlete and will continue as a working mum, focusing on the media and other work that has always sat as part of my double career track alongside athletics.
"2014 is obviously a huge year for Scotland and this was not an easy decision to make as it means not competing in a home Commonwealth Games.
"Now is my time however. I am excited for the new opportunities and challenges that retiring from athletics will bring me and look forward to getting involved with a home games - just not as a competing athlete."
McConnell has won more major championship medals than any other Scottish athlete with nine, including Commonwealth silver in 2002 and two World Champion relay bronzes.
Scottishathletics paid tribute to McConnell's dedication throughout more than a decade at the top level.
Chief executive Nigel Holl said: "Lee has been arguably Scotland's most successful track and field athlete for the past decade or more, with medals from a number of major championships - Commonwealth, European and world.
"She has shown that level of success can be achieved whilst staying based in Scotland - with a Scottish coach (Rodger Harkins) throughout her career - and she should be rightly recognised for her achievements, consistency of performance, and dedication to athletics."
Holl added: "I hope and expect there is a role for Lee within athletics in the future - sharing her experiences with future Scottish athletes. When the time is right, we very much look forward to having that conversation with her."
Director of coaching Stephen Maguire admitted McConnell's absence from Glasgow 2014 would be a major loss but he believes her example can have a wider benefit.
Maguire said: "This is very unfortunate for us from a sporting point of view because Lee has been a great Scottish athlete for a number of years and the Commonwealth Games in her home city of Glasgow would have been the perfect way to close her career.
"Her vast experience would have been invaluable to Team Scotland's track and field team and I'm very disappointed we won't benefit from that.
"But I firmly support Lee in her decision. From a personal point of view, her own welfare and her family must come first.
"The mental strength, and commitment to training, required to keep on making selections is significant and she has set a wonderful example in that regard to the next generation of Scottish athletes."