| Round of 32 | ||||
| Eastern Bracket | ||||
| 12/8/40 | Passon SC (Phi.) | 6 : 3 | Ruggiero SC (Bal.) | |
| 12/15/40 | Prague SC (NYC) | 5 : 3 | Bigelow Sanford (NY) | |
| 12/15/40 | Danish FC (NYC) | 1 : 5 | S.A. Healey (NY) | |
| 12/29/40 | Gjoa FC (NYC) | 3 : 2 | Swedish SC (NYC) | |
| 2/1/41 | Fall River SC | 4 : 1 | Stamford (CT) | |
| 12/15/40 |
Pawtucket Rangers | 2 : 1 |
Lusitania Recreation | |
| Hosiery Local (Phi.) | ||||
| German Hungarian SC (NYC) | ||||
| Western Bracket | ||||
| 11/17/40 | Sparta Ogden Dairy (Chi.) | 2 : 0 | Viking A.A. (Chi.) | |
| 11/24/40 | Slovak SC (Chi.) | 1 : 0 | Wacker FC (Mil.) | |
| 12/8/40 | Chrysler SC (Det.) | 2 : 0 | Dalarda (Cle.) | |
| 11/17/40 | United German American AA (Det.) | 2 : 0 | Thistles SC (Det.) | |
| 11/17/40 | Morgan Strasser (W. Pa.) | 3 : 0 | Glendale (W. Pa.) | |
| Gallatin-Dunlevy (W. Pa.) | ||||
| Buffalo City GOP | ||||
| ??? | ||||
| Round of 16 | ||||
| Eastern Bracket | ||||
| 1/12/41 | Passon SC | 2 : 0 | Hosiery Local FC | |
| 1/19/41 | German Hungarian FC | 4 : 2 | S.A. Healy FC | |
| 1/19/41 |
Pawtucket Rangers | 2 : 0 |
Fall River FC | |
| 2/24/41 | Gjoa FC | 2 : 2 | Prague FC | |
| 3/2/41 | R | Gjoa FC | 1 : 1 | Prague FC |
| 3/16/41 | R | Gjoa FC | 2 : 2 | Prague FC |
| 3/23/41 | R | Gjoa FC | 1 : 0 | Prague FC |
| Western Bracket | ||||
| 12/15/40 | Morgan Strasser | 1 : 2 | Gallatin-Dunlevy | |
| 12/8/40 | Chrysler FC | 1 : 0 | United German American AA | |
| 12/8/40 | Sparta Ogden Dairy | 2 : 1 | Slovak SC | |
| Buffalo City GOP | W : L | |||
| Quarterfinals | ||||
| 3/23/41 | Passon SC | 3 : 1 | German Hungarian FC | |
| 3/23/41 | Sparta Ogden Dairy | 1 : 3 | Gallatin-Dunlevy | |
| 3/30/41 | Pawtucket Rangers | 3 : 0 |
Gjoa FC | |
| 3/23/41 | Chrysler FC | 4 : 2 | Buffalo City GOP | |
| Semifinals | ||||
| 4/13/41 | 1L | Pawtucket Rangers | 3 : 0 | German Hungarian FC |
| 4/20/41 | 2L | German Hungarian FC | 1 : 5 | Pawtucket Rangers |
| Pawtucket Rangers advance on 8-1 aggregate | ||||
| 4/7/41 | 1L | Gallatin-Dunlevy | 1 : 3 | Chrysler FC |
| 4/14/41 | 2L | Chrysler FC | 2 : 0 | Gallatin-Dunlevy |
| Chrysler SC advance on 5-1 aggregaste | ||||
| Final | ||||
| First Leg – at Pawtucket Rhode Island | ||||
| 5/4/41 | Pawtucket Rngers | 4 : 2 | Chrysler FC | |
| Second Leg – at Detroit, Michigan | ||||
| 5/11/41 | Chrysler FC | 3 : 4 (aet) | Pawtucket Rangers | |
| Aggregate drawn 5-5, Pawtucket Rangers win National Challenge Cup on 8-5 aggregate after extra time | ||||
| KEY – w/o – Walkover, R – Replay, 1L – 1st Leg, 2L – 2nd Leg, 3L – 3rd Leg | ||||