| Europa League Qual. | M. | W | D | L | goals | |||
| at home | 1 | 0 | 0 | 1 | 0 | : | 1 | |
| Away | 2 | 0 | 0 | 2 | 1 | : | 4 | |
| ∑ | 3 | 0 | 0 | 3 | 1 | : | 5 | |
| overall | M. | W | D | L | goals | |||
| at home | 1 | 0 | 0 | 1 | 0 | : | 1 | |
| Away | 2 | 0 | 0 | 2 | 1 | : | 4 | |
| Neutral Place | 0 | 0 | 0 | 0 | 0 | : | 0 | |
| ∑ | 3 | 0 | 0 | 3 | 1 | : | 5 | |
| Europa League Qual. | |||||
| 2020/2021 | Play-offs | Dinamo Zagreb | - | FC Flora | 3:1 (2:0) |
| 2001/2002 | Qualifier | FC Flora | - | Dinamo Zagreb | 0:1 (0:1) |
| 2001/2002 | Qualifier | Dinamo Zagreb | - | FC Flora | 1:0 (0:0) |
|
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}
