Evanilson Gomes da Costa, described as a gang leader, was reportedly killed after being shot in the remote town of Coari, close to where Emma Kelty went missing.
The 24-year-old pirate, who according to reports went by the name of 'Baia', died in hospital.
British adventurer Kelty was last heard from on September 13, days after posting about her fears of being robbed or murdered in a jungle area in Brazil's remote north used for drug trafficking.
Ivo Martins, head of the Amazonas state homicide division, told the Associated Press she was killed after being robbed and her body was thrown in the Solimoes River.
Ms Kelty was 42 days into a 4,000-mile trip from the Amazon's source in Peru, through Brazil and to its mouth on the Atlantic Ocean, using a GPS tool, social media and blogging to let friends follow her progress.