On 11 July 2013, Vasco da Gama announced Juninho's return to the club. The player scored and assisted in his third debut for Vasco, in a 3–1 victory against rivals Fluminense. He scored his first home goal of the season against Criciúma with a 32-metre free kick, also assisting Edmílson for the third goal of the game. He played his third game for Vasco da Gama against another rival team Botafogo, setting up Andre for Vasco's first goal, in a 3–2 defeat. He played his sixth game against Grêmio and made another assist. It was his fourth assist in Campeonato Brasileiro. Juninho made his fifth assist against Sport Club Corinthians Paulista; the game ended in a 1–1 draw. He played his 16th game against Vasco rivals Botafogo and made two assists; the game ended with a 2–2 draw after Botafogo had led 2–0. Juninho played 16 games for Vasco in his third stint with the club, scoring 2 goals and making 7 assists in the Campeonato Brasileiro.