At the 2016 FINA World Swimming Championships in Windsor, Ontario, Canada, Scheffer finished 25th in the Men's 200 metre freestyle, 33rd in the Men's 400 metre freestyle and 40th in the Men's 100 metre freestyle. On April 27, 2018, participating in the Maria Lenk Trophy competition in Rio de Janeiro, Scheffer broke the South American record in the 200-metre freestyle race in 1:46.08 seconds. Three days later, he broke the South American record in the 400-metre freestyle race in 3:49.06 seconds. At the 2018 South American Games in Cochabamba, he won two gold medals in the 200m and 4 × 200 m freestyle, and a silver medal at the 4 × 100 m freestyle. At the 2018 Pan Pacific Swimming Championships in Tokyo, Japan, Scheffer made his first major involvement in an international tournament, finishing 4th in the Men's 200 metre freestyle, 4th in the Men's 4 × 200 metre freestyle relay and 6th in the Men's 400 metre freestyle. On August 25, 2018, participating in the José Finkel Trophy competition in São Paulo, Scheffer broke the South American record in the 400-metre freestyle race in 3:40.87 seconds. At the 2018 FINA World Swimming Championships in Hangzhou, China, Fernando Scheffer, along with Luiz Altamir Melo, Leonardo Coelho Santos and Breno Correia, surprised the world by winning the gold medal in the Men's 4 × 200 metre freestyle relay, breaking the world record, with a time of 6:46.81. The relay was composed only by young people between 19 and 23 years, and was not favorite to gold. In the Men's 400 metre freestyle, he broke the South American record at heats, with a time of 3:39.10. He finished 8th in the final. On 21 December 2018, at the Porto Alegre Open in Brazil, he broke the long course South American record in the 200-metre freestyle, with a time of 1:45.51. It was the fourth fastest time in the world in 2018. He broke five South American records in 2018. At the 2019 World Aquatics Championships in Gwangju, South Korea, Brazil's young 4 × 200 metre freestyle relay team, now with João de Lucca instead of Leonardo Coelho Santos, lowered the South American record in almost 3 seconds, with a time of 7:07.12, at heats. They finished 7th, with a time of 7:07.64 in the final. It was the first time that Brazil's 4x200m freestyle relay had qualified for a World Championships final, and the result qualified Brazil for the Tokyo 2020 Olympics.In the Men's 200 metre freestyle, he was very close to qualify for the final, finishing 9th, just 8 milliseconds from 8th place. He swam near his South American record, finishing 1:45.83 in the semifinals. At the 2019 Pan American Games held in Lima, Peru, Scheffer won two gold medals in the Men's 200 metre freestyle and in the Men's 4 × 200 metre freestyle relay, breaking the Pan American Games record in the relay. He also won the silver medal in the Men's 400 metre freestyle.
