| Round of 32 | ||||
| Eastern Bracket | ||||
| 2/10/46 | Brooklyn Wanderers | 2: 1 | German Hungarian SC (NYC) | |
| 3/10/46 | Brooklyn Hispano | 3 : 0 | Hakoah SC (NYC) | |
| 3/17/46 | Baltimore SC | 4 : 2 | Ruggiero SC (Bal.) | |
| 3/17/46 | Baltimore Americans | 6 : 1 | Hasslinger SC (Bal.) | |
| 4/21/46 | New York Americans | 5 : 1 | Eintracht SC (NYC) | |
| 4/21/46 | Kearny Americans | 1 : 0 | Elizabeth SC | |
| Ponta Delgada | ||||
| Philadelphia Americans | ||||
| Western Bracket | ||||
| 1/6/46 | Castle Shannon (W. Pa.) | 4 : 3 | Morgan Strasser (W. Pa.) | |
| 1/13/46 | Heidelberg Losegos (W. Pa.) | 2 : 1 | Sturgeon (W. Pa.) | |
| Replay ordered after Sturgeon protest was upheld | ||||
| 1/27/46 | R | Heidelberg Losegos | 9 : 1 | Sturgeon |
| 3/17/46 | Cleveland Americans | 7 : 1 | Becks German American SC (Buf.) | |
| 3/24/46 | Sparta (Chi.) | 7 : 1 | Schlitz SC (Mil.) | |
| 3/24/46 | Viking AA (Chi.) | 6 : 2 | Necaxa (Chi.) | |
| Pioneer Kickers (Det.) | ||||
| Carondelet (St. L) | ||||
| 2/10/46 |
Raferty Painters (St. L) | 2 : 1 |
Natural Set Ups | |
| Round of 16 | ||||
| Eastern Bracket | ||||
| 4/28/46 | 1L | Ponta Delgada | 2 : 0 | New York Americans |
| 5/5/46 | 2L | New York Americans | 2 : 3 | Ponta Delgada |
| Ponta Delgada advance on 5-2 aggregate | ||||
| 5/5/46 | Brooklyn Wanderers | 3 : 0 | Brooklyn Hispanos | |
| 5/5/46 | Baltimore Americans | w/o | Baltimore SC | |
| 4/28/46 | 1L | Philadelphia Americans | 1 : 0 | Kearny Scots |
| 5/5/46 | 2L | Philadelphia Americans | 2 : 2 | Kearny Scots |
| Philadelphia Americans advance on 3-2 aggregate | ||||
| Western Bracket | ||||
| 2/10/46 | Heidelberg Losegos | 1 : 0 | Castle Shannon | |
| 3/31/46 | Viking AA | 2 : 1 (aet) | Sparta | |
| 4/13/46 |
Carondelet | 4 : 2 |
Raferty | |
| 4/14/46 | Cleveland Americans | 0 : 0 (aet) | Pioneer Kickers | |
| 4/21/46 | R | Cleveland Americans | 2 : 1 (aet) | Pioneer Kickers |
| Quarterfinals | ||||
| 4/28/46 | Viking A.A. | 1 : 0 | Carondolet | |
| 5/26/46 | 1L | Brooklyn Wanderers | 1 : 2* | Ponta Delgada |
| *Match protested by Brooklyn over a shortage of eight minutes playing time in the first half. | ||||
| Match replayed after second leg. | ||||
| 6/3/46 | 2L | Ponta Delgada | 1 : 1 | Brooklyn Wanderers |
| 6/17/46 | 1LR | Brooklyn Wanderers | 1 : 3 | Ponta Delgada |
| Ponta Delgada advance on 4-2 aggregate | ||||
| 6/10/46 | Philadelphia Americans | 4 : 2 |
Baltimore Americans | |
| 4/28/46 | Heidelberg Losegos | 2 : 1 (aet) | Cleveland Americans | |
| Semifinals | ||||
| 6/23/46 | 1L | Ponta Delgada | 4 : 2 | Philadelphia Americans |
| 6/30/46 | 2L | Philadelphia Americans | 3 : 2 | Ponta Delgada |
| Ponta Delgada advance on 6-5 aggregate | ||||
| 5/12/46 | 1L | Heidelberg S.C. | 3 : 1 | Viking A.A. |
| 5/20/46 | 2L | Viking A.A. | 2 : 0(aet) | Heidelberg S.C. |
| 5/27/46 | 3L | Viking A.A. | 3 : 1 | Heidelberg S.C. |
| Viking AA advance on 6-4 aggregate | ||||
| Final | ||||
| First Leg – at Mark’s Stadium – Tiverton, Rhode Island | ||||
| 7/7/46 | Ponta Delgada | 1 : 1 | Viking A.A. | |
| Second Leg – at Comiskey Park – Chicago, Illinois | ||||
| 7/14/46 | Viking A.A. | 2 : 1 | Ponta Delgada | |
| Viking AA win National Challenge Cup on 3-2 aggregate | ||||
| KEY – w/o – Walkover, R – Replay, 1L – 1st Leg, 2L – 2nd Leg, 3L – 3rd Leg | ||||