At only 14 years old, she collected two gold medals at the 5 km and 10 km marathon, at the 2006 South American Games in Buenos Aires.
In 2005, she was able to reach second place in Travessia dos Fortes (the most important competition of the aquatic marathon calendar in Brazil). Subsequently, became champion in 2006 and 2011.
Cunha qualified for the 2008 Summer Olympics in Beijing, after placing tenth at the FINA World Open Water Swimming Championships in Seville, Spain. She became the youngest-ever swimmer to participate in the inaugural women's 10 km open water marathon, against a field of twenty-four other competitors, including her teammate Poliana Okimoto, South African amputee Natalie du Toit, British duo Keri-Anne Payne and Cassandra Patten, and sixteen-year-old American Chloe Sutton. Cunha finished in a close race for fifth place, with a total time of 1:59:36.8, approximately one second ahead of Switzerland's Swann Oberson, yet nine seconds behind winner Larisa Ilchenko of Russia.
At the 2009 FINA World Championships in Rome, Italy, Cunha finished twenty-second in the 10 km marathon, with a time of 2:02:06.4. The following year, she reinforced her lead in the FINA 10 km Marathon Swimming World Cup circuit, by dominating all eight meets of the series. Because of her repeated successes, Cunha was selected as FINA's best female open water swimmer of the year.
She won the gold medal at the 5 km marathon tied with Andreina Pinto, at the 2010 South American Games in Medellín. She also got the silver medal in the 10 km marathon.
At the 2011 FINA World Championships in Shanghai, Cunha won the gold medal in the women's 25 km marathon, with a time of 5:29:22.9. Despite of her first world championship success, Cunha nearly missed out of the final slot for the 2012 Summer Olympics in London, as she placed eleventh in the 10 km marathon, with a slowest time of 2:02:22.2, four seconds behind Spain's Erika Villaécija García. Cunha also placed seventh in the 5 km marathon with a time of
In 2012, Cunha decided to withdraw from the FINA Olympic Marathon Swim Qualifier, held in Setubal, Portugal, to focus on her competitive career for the FINA 10 km Marathon Swimming World Cup circuit. She dominated the series by successfully defending her title for the second time, amassing a total of 160 points and four victories in eight different meets.
At the 2013 FINA World Championships in Barcelona, Spain, Cunha handed an entire medal haul for the Brazilians in the 5 km marathon, as she snatched the bronze in 56:44.4. Three days later, she won the silver medal in the 10 km marathon, with her teammate Poliana Okimoto winning the gold medal. Ending her participation, she was in the 25 km marathon, where she tried to defend her 2011 title, but finished in fifth place, 4 seconds of the race winner.
At the 2015 FINA World Championships in Kazan, Cunha won a bronze medal in the 10 km marathon. Two days later, she won the silver medal in the Mixed 5km Team Event. On August 1, she became two-time World Champion of the 25 km marathon. At 23, Ana Marcela Cunha became the Brazilian woman with more medals won at the World Championships of Olympic sports.
Returning to the Olympic open water marathon in 2016, Cunha was deemed the race's favorite in previews. She finished in tenth, blaming the underperformance on missing the in-race nutrition.
At the 2017 FINA World Championships in Budapest, Cunha won two bronze medals in the 5 km matathon and in the 10 km marathon.. On July 21, she became three-time World Champion of the 25 km marathon. She also participated at the Mixed 5km Team Event, along with Viviane Jungblut, Allan do Carmo and Fernando Ponte, finishing 6th.