| Champions League Qual. | M. | W | D | L | goals | |||
| at home | 1 | 0 | 1 | 0 | 0 | : | 0 | |
| Away | 1 | 0 | 0 | 1 | 0 | : | 1 | |
| ∑ | 2 | 0 | 1 | 1 | 0 | : | 1 | |
| Conference League Qual. | M. | W | D | L | goals | |||
| at home | 1 | 1 | 0 | 0 | 4 | : | 2 | |
| Away | 1 | 1 | 0 | 0 | 1 | : | 0 | |
| ∑ | 2 | 2 | 0 | 0 | 5 | : | 2 | |
| overall | M. | W | D | L | goals | |||
| at home | 2 | 1 | 1 | 0 | 4 | : | 2 | |
| Away | 2 | 1 | 0 | 1 | 1 | : | 1 | |
| Neutral Place | 0 | 0 | 0 | 0 | 0 | : | 0 | |
| ∑ | 4 | 2 | 1 | 1 | 5 | : | 3 | |
| Champions League Qual. | |||||
| 2011/2012 | 2. Round | FC Flora | - | Shamrock Rovers | 0:0 (0:0) |
| 2011/2012 | 2. Round | Shamrock Rovers | - | FC Flora | 1:0 (1:0) |
| Conference League Qual. | |||||
| 2021/2022 | Play-offs | Shamrock Rovers | - | FC Flora | 0:1 (0:0) |
| 2021/2022 | Play-offs | FC Flora | - | Shamrock Rovers | 4:2 (2:1) |
|
For games that were decided on penalties the score after 120 minutes will be included in the ranking |
Estonia 
![FC Flora [Women]](https://s.hs-data.com/bilder/wappen/mini/30430.gif?fallback=png "FC Flora [Women]"){kind=small}
![FC Flora [Youth]](https://s.hs-data.com/bilder/wappen/mini/24240.gif?fallback=png "FC Flora [Youth]"){kind=small}
