| 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 | |
| Europa League Qual. | M. | W | D | L | goals | |||
| at home | 1 | 1 | 0 | 0 | 2 | : | 0 | |
| Away | 1 | 0 | 0 | 1 | 0 | : | 5 | |
| ∑ | 2 | 1 | 0 | 1 | 2 | : | 5 | |
| overall | M. | W | D | L | goals | |||
| at home | 2 | 1 | 1 | 0 | 2 | : | 0 | |
| Away | 2 | 0 | 0 | 2 | 0 | : | 6 | |
| Neutral Place | 0 | 0 | 0 | 0 | 0 | : | 0 | |
| ∑ | 4 | 1 | 1 | 2 | 2 | : | 6 | |
| Champions League Qual. | |||||
| 2002/2003 | 1. Round | APOEL Nikosia | - | FC Flora | 1:0 (0:0) |
| 2002/2003 | 1. Round | FC Flora | - | APOEL Nikosia | 0:0 (0:0) |
| Europa League Qual. | |||||
| 2018/2019 | 2. Round | FC Flora | - | APOEL Nikosia | 2:0 (2:0) |
| 2018/2019 | 2. Round | APOEL Nikosia | - | FC Flora | 5:0 (2:0) |
|
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}
