The 2017 Copa Sudamericana second stage was played from 27 June to 9 August 2017. A total of 32 teams competed in the second stage to decide the 16 places in the final stages of the 2017 Copa Sudamericana.

The draw for the second stage was held on 14 June 2017, 20:00 PYT (UTC−4), at the CONMEBOL Convention Center in Luque, Paraguay. For the second stage, the teams were allocated to two pots according to their previous results in this season:

The 32 teams were drawn into 16 ties (O1–O16) between a team from Pot 1 and a team from Pot 2, with the teams from Pot 1 hosting the second leg. Teams from the same association could be drawn into the same tie.

The following were the 10 teams transferred from the Copa Libertadores (two best teams eliminated in the third stage of qualifying and eight third-placed teams in the group stage).

The following were the 22 winners of the first stage from the Copa Sudamericana. Matches in the first stage were considered for the ranking of teams for the second stage draw.

In the second stage, each tie was played on a home-and-away two-legged basis. If tied on aggregate, the away goals rule would be used. If still tied, extra time would not be played, and the penalty shoot-out would be used to determine the winner (Regulations Article 6.1).

The 16 winners of the second stage advanced to the round of 16 of the knockout stages.

The first legs were played on 27–29 June, 5–6 and 11–13 July, and the second legs were played on 25–27 July, 1–3 and 9 August 2017.