Lynn began to skate almost as soon as she could walk and took part in her first exhibition performance at the age of four in a group number at Chicago Stadium. By age seven, she was living away from home part of the year, staying with the slightly older skater Jada Steinke to be close to her coach Slavka Kohout, who worked out of Rockton, Illinois, but her close-knit family was never far away. Eventually her family moved from the Chicago suburb of Evergreen Park to Rockford, Illinois, some fifteen miles from Rockton and the rink. Janet would attend Junior High in Rockford. She used her middle name Lynn instead of Nowicki, which was constantly being misspelled and mispronounced. Janet was always forthright about the name change; in her own mind her name was still Nowicki.

In 1964, at 11, she became the youngest skater to pass the rigorous eighth and final test administered by the United States Figure Skating Association, and two years later she won the U.S. Junior Ladies Championship at Berkeley, California. At that competition she landed a triple salchow jump, which at the time was rarely performed by female skaters, giving early evidence of a jumping ability that was to thrill audiences and impress judges for years to come. In later years she was also one of the first female skaters to include a triple toe loop in her programs.

Moving up to senior level, Lynn gained 3rd place at the 1968 U.S. Championships, which qualified her to compete at the 1968 Winter Olympics in Grenoble, France, where she placed 9th. At the time she was 14 years old and it was her first major international competition. She also placed 9th at her first World Championships in 1968.

Lynn won her first Senior national title at the 1969 U.S. Figure Skating Championships.

That year she beat Canada's Karen Magnussen for the North American Championship, but had disappointing results in the World Championships. Despite the absence of both Magnussen and Czechoslovakia's Hana Maskova due to injuries, Lynn was unable to do better than 5th place, falling behind Julie Lynn Holmes, in 4th, whom she had beaten for the national title. Gabriele Seyfert of East Germany took the gold medal.

The World Championships were to remain a problem for her. Although she continued to reign as U.S. Champion, something always seemed to go wrong at Worlds. In 1970, Seyfert and Austria's Beatrix Schuba were again in 1st and 2nd place, while Holmes moved up to 3rd and Lynn dropped back to 6th. Part of the problem was an inconsistency in compulsory figures, which meant that she always had to make up ground in the free skating. Lynn made an effort to remedy this weakness by working with the great New York-based coach Pierre Brunet, who had previously had World Champions Carol Heiss and Donald Jackson under his tutelage. At the 1971 World Championships, she placed 5th in figures and skated well in the free skating to place 4th overall, while Schuba took the gold, Holmes the silver and Magnussen the bronze.

The year 1972 brought both World and Olympic challenges. Lynn beat Holmes for the national title for the fourth year in a row, and there were widespread predictions that she would finally take not only World but Olympic gold, especially because of Schuba's weakness in free skating. Schuba's lackluster performance at Lyon, France the previous year had even drawn boos, but she won the championship based on her enormous lead in the compulsory figures.

At the 1972 Winter Olympics at Sapporo, Hokkaidō, Japan, Lynn placed a disappointing 4th in the compulsory figures. Once again Schuba's technical mastery in this discipline was very strong; although she placed only 7th in the free skating, her large lead from the figures enabled her to take the gold medal. Magnussen won the silver and Lynn was left with the bronze, an order of finish repeated at the 1972 World Championships in Calgary, Alberta, Canada.

By this time, international-level disappointments had taken their toll, and Lynn was also struggling with her weight and lack of motivation that nearly caused her to quit skating. But she had always had a very strong Christian faith and a belief that God had given her a gift for skating with an intention that she use it. After considerable soul-searching, she continued, taking her fifth National title in 1973. With Schuba's retirement and the devaluation of compulsory figures caused by the addition of the short program to competitions, only Magnussen seemed to stand in her way.

At the 1973 World Championships, Lynn skated her best figures ever, taking 2nd in that discipline, but in the newly-introduced short program of required jumps and spins, which she had been expected to win, two falls landed her in 12th position. She came out on top in free skating, but the short program kept her from the gold. A silver medal would mark the end of Lynn's amateur career.