| Group I | 15/09/2016 | OGC Nice | - | FC Schalke 04 | 0:1 | ||||
| Group I | 29/09/2016 | FC Schalke 04 | - | RB Salzburg | 3:1 | ||||
| Group I | 20/10/2016 | FK Krasnodar | - | FC Schalke 04 | 0:1 | ||||
| Group I | 03/11/2016 | FC Schalke 04 | - | FK Krasnodar | 2:0 | ||||
| Group I | 08/12/2016 | RB Salzburg | - | FC Schalke 04 | 2:0 | ||||
| Round of 32 | 16/02/2017 | PAOK Saloniki | - | FC Schalke 04 | 0:3 |  |
|||
| Round of 32 | 22/02/2017 | FC Schalke 04 | - | PAOK Saloniki | 1:1 |  |
|||
| Round of 16 | 09/03/2017 | FC Schalke 04 | - | Bor. Mönchengladbach | 1:1 | ||||
| Round of 16 | 16/03/2017 | Bor. Mönchengladbach | - | FC Schalke 04 | 2:2 | ||||
| Quarter-finals | 13/04/2017 | AFC Ajax | - | FC Schalke 04 | 2:0 |
Austria