The 81-year-old ex-player known as "O Rei" (The King) "is stable and will continue the treatment of the colon tumour that was identified in September of this year," the Albert Einstein Hospital said in a statement.
Pele underwent surgery for the tumour on September 4, spending a month in the hospital before being discharged to continue chemotherapy.
It is the latest in a string of health troubles for the ageing star, whose public appearances have grown increasingly rare.
Considered by many the greatest footballer of all time, Edson Arantes do Nascimento -- Pele's real name -- is the only player in history to win three World Cups (1958, 1962 and 1970).
He burst onto the global stage at just 17 by scoring dazzling goals, including two in the final against hosts Sweden, as Brazil won the World Cup for the first time in 1958.
He went on to have one of the most storied careers in sport, scoring more than 1,000 goals before retiring in 1977.
Pele announced on Instagram on December 9 that he would stay in the hospital for just "a few days" for chemotherapy.
He ended up staying for two weeks. "Don't worry, I'm just getting ready for the holiday season!" he said in a message to fans.