| Round of 32 | ||||
| Eastern Bracket | ||||
| 1/9/39 | Baltimore SC | 4 : 0 | Brooklyn Hakoah | |
| 1/9/39 | Brooklyn Hispano | 1 : 2 | Holy Cross (Fall River) | |
| 1/9/39 | Brookhattan (NYC) | 4 : 1 | Bethlehem Hungarian SC | |
| 1/9/39 | German American SC (Phi.) | 2 : 1 | Baltimore German SC | |
| 1/9/39 | Trenton Highlanders | 2 : 0 | Kearny Irish | |
| 1/29/39 | New York Americans | 1 : 3 | St. Mary’s Celtic (Brooklyn) | |
| 2/5/39 | Passon SC (Phi.) | 3 : 3 | Kearny Scots | |
| 2/10/39 | R | Kearny Scots | 3 : 2 | Passon SC (Phi.) |
| 1/8/39 |
Lusitania Recreation | 4 : 3 |
St. Michael’s | |
| 1/22/39 | Lusitania Recreation | 1 : 0 | St. Michael’s | |
| Western Bracket | ||||
| 12/11/38 | Sparta Garden City (Chi.) | 1 : 0 | Olympia SC (Chi.) | |
| 12/11/38 | Manahttan Beer (Chi.) | 4 : 0 | Swedish American SC (Chi.) | |
| 12/11/38 | German Sport Club (W. Pa.) | 3 : 0 | Curry (W. Pa) | |
| 12/11/38 | Morgan Sports Club (Pit.) | 2 : 1 | Heidelberg (W. Pa.) | |
| 12/11/378 | Shamrock SC (Cle.) | 2 : 2 | Bartunek Slavia (Cle.) | |
| 12/18/38 | R | Shamrock SC | 0 : 0 (aet) | Bartunek Slavia |
| 1/2/39 | R | Shamrock SC | 1 : 5 | Bartunek Slavia |
| Kodak Park (Roch.) | ||||
| 12/11/38 |
Lindell Trust (St. L) | 3 : 1 |
Burke(St. L) | |
| Chrysler SC (Det.) | ||||
| Round of 16 | ||||
| Eastern Bracket | ||||
| 2/12/39 | German American SC | 1 : 0 | Baltimore SC | |
| 2/12/39 | St. Mary’s Celtic | 6 : 4 (aet) | Trenton Highlanders | |
| 3/19/39 | Brookhattan | 1 : 0 | Kearny Scots | |
| 2/12/39 |
Lusitania Recreation | 1 : 1 |
Holy Cross | |
| 2/19/39 |
Lusitania Recreation | 2 : 1 |
Holy Cross | |
| Western Bracket | ||||
| 1/8/39 | Sparta Garden City | 7 : 1 | Lindell Trust | |
| 1/8/39 | Manhattan Beer | 4 : 2 | Chrysler SC | |
| 1/8/39 | German Sport Club | 1 : 1 (aet) | Morgan Sport Club | |
| 1/15/39 |
R | Morgan Sport Club | 5 : 0 | German Sport Club |
| 1/8/39 | Kodak Park | 1 : 1 (aet) | Bartunek Slavia | |
| 1/15/39 | R | Bartunek Slavia | 3 : 0 | Kodak Park |
| Quarterfinals | ||||
| 3/12/39 | Manhattan Beer | 3 : 2 | Bartunek Slavia | |
| 3/12/39 | Morgan Sport Club | 4 : 2 | Sparta A & BA | |
| 3/26/39 | German American SC | 3 : 2 (aet) | Lusitania Recreation | |
| 4/2/39 | Brookhattan | 1 : 3 | St. Mary’s Celtic | |
| Semifinals | ||||
| 4/15/39 | 1L | German American SC | 0 : 2 | St. Mary’s Celtic |
| 4/16/39 | 2L | St. Mary’s Celtic | 1 : 2 | German American SC |
| St. Mary’s Celtic advance on 3-2 aggregate | ||||
| 4/2/39 | 1L | Morgan Sport Club | 3 : 2 | Manhattan Beer |
| 4/19/39 | 2L | Manhattan Beer | 3 : 1 | Morgan Sport Club |
| Manhattan Beer advance on 5-4 aggregate | ||||
| Final | ||||
| First Leg – at Sparta Stadium – Chicago, Illinois | ||||
| 4/30/39 | Manhattan Beer | 0 : 1 | St. Mary’s Celtic | |
| Second Leg – Starlight Park – Bronx, New York | ||||
| 5/7/39 | St. Mary’s Celtic | 4 : 1 | Manhattan Beer | |
| St. Mary’s Celtic win National Challenge Cup on 5-2 aggregate | ||||
| KEY – w/o – Walkover, R – Replay, 1L – 1st Leg, 2L – 2nd Leg, 3L – 3rd Leg | ||||