| Club: | Flamurtari Vlorë |
| Season: | 2016–17 |
| Manager: | Gugash Magani (until 17 October 2016) Gentian Mezani (from 25 October 2016 to 16 February 2017) Shpëtim Duro (from 17 February 2017) |
| Chairman: | Sinan Idrizi |
| Stadium: | Flamurtari Stadium |
| League: | Kategoria Superiore |
| League Result: | 8th |
| Cup1: | Albanian Cup |
| Cup1 Result: | Quarter-finals |
| League Topscorer: | Tomislav Bušić (10) |
| Season Topscorer: | Tomislav Bušić (12) |
| Prevseason: | 2015–16 |
| Nextseason: | 2017–18 |
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This article covers the 2016–17 season for Flamurtari Vlorë. They'll participate in the Kategoria Superiore and Albanian Cup.[1]
Squad at end of season[2]
| Date | Pos. | Name | From | Fee |
|---|---|---|---|---|
| 1 July 2016 | FW | Astrit Fazliu |  Partizani Tirana | Undisclosed [3] |
| 1 July 2016 | MF |  Balša Radović | Lovćen | Undisclosed [4] |
| 1 July 2016 | MF |  Masaki Iinuma | Free agent | Free |
| 4 July 2016 | MF | Donjet Shkodra |  Deinze | Undisclosed [5] |
| 4 July 2016 | DF |  Miloš Rnić | Metalac Gornji Milanovac | Undisclosed |
| 5 July 2016 | FW | Tomislav Bušić | Free agent | Free [6] |
| 7 July 2016 | GK | Ibrahim Bejte | Besëlidhja Lezhë | Undisclosed [7] |
| 12 July 2016 | MF | Alessio Hyseni |  Perugia | Undisclosed [8] |
| 21 July 2016 | DF | Franc Veliu | Partizani Tirana | Undisclosed [9] |
| 29 July 2016 | DF | Nikola Đurić | Rad | Undisclosed [10] |
| 20 August 2016 | FW | Ivan Galić |  Rabotnički | Undisclosed [11] |
| 30 August 2016 | GK | Stivi Frashëri | Bylis Ballsh | Undisclosed |
| 8 January 2017 | DF | Ivan Jakovljević |  Radnik Bijeljina | Undisclosed |
| 27 January 2017 | DF | Ergis Mersini | Luftëtari Gjirokastër | Free |
| 30 January 2017 | MF | Haxhi Neziraj | Free agent | Free |
| 31 January 2017 | FW |  Lynneeker | Free agent | Free |
| 31 January 2017 | DF | Mauricio Leal |  Sriwijaya | Undisclosed |
| Date | Pos. | Name | To | Fee |
|---|---|---|---|---|
| 1 July 2016 | MF | Bedri Greca | Kukësi | Free [12] |
| 1 July 2016 | DF | Debatik Curri | Prishtina | Undisclosed [13] |
| 1 July 2016 | DF | Hektor Idrizaj | Skënderbeu | Undisclosed [14] |
| 1 July 2016 | MF | Ignacio Nicolini | Released | Free [15] |
| 1 July 2016 | MF | Lorik Maxhuni | Prishtina | Undisclosed [16] |
| 28 July 2016 | MF | Yll Hoxha | Vllaznia Shkodër | Undisclosed [17] |
| 2 August 2016 | DF | Entonio Pashaj | Kukësi | Undisclosed [18] |
| 2 August 2016 | FW | João Henrique | Portuguesa | Free [19] |
| 5 December 2016 | DF | Slavko Lukić | Released | Free |
| 31 January 2017 | DF | Kristi Marku | Partizani Tirana | Free |
See main article: 2016–17 Kategoria Superiore.
See main article: 2016–17 Albanian Cup.