| Competition: | Macedonian Second League |
| Season: | 2016–17 |
| Winners: | Akademija Pandev |
| Promoted: | Akademija Pandev Skopje |
| Relegated: | Metalurg Vardar Negotino |
| Biggest Home Win: | Akademija Pandev 7–0 Tikvesh |
| Biggest Away Win: | Novaci 0–4 Horizont Turnovo |
| Highest Scoring: | Akademija Pandev 7–0 Tikvesh Novaci 2–5 Akademija Pandev |
| Matches: | 135 |
| Total Goals: | 335 |
| League Topscorer: | Zoran Baldovaliev (20 goals) |
| Longest Wins: | 10 games Akademija Pandev |
| Longest Unbeaten: | 10 games Akademija Pandev |
| Longest Winless: | 13 games Metalurg |
| Longest Losses: | 5 games Metalurg |
| Prevseason: | 2015–16 |
| Nextseason: | 2017–18 |
The 2016–17 Macedonian Second Football League was the 25th season of the Macedonian Second Football League, the second division in the Macedonian football league system. It began on 13 August 2016 and ended on 27 May 2017. It was the last season with the current format, as of 2017–18 season the league will be divided into two groups, East and West, for the first time since the 1999–2000 season, with 10 teams in each group instead of the single league structure.[1]
| Club | City | Stadium | Capacity |
|---|---|---|---|
| Akademija Pandev | Strumica | Stadion Mladost | 6,500 |
| Euromilk Gorno Lisiche | Skopje | Stadion Cementarnica | 2,000 |
| Metalurg | Skopje | Stadion Zhelezarnica | 3,000 |
| Novaci 1 | Novaci | Stadion Novaci | 500 |
| Skopje | Skopje | Stadion Avtokomanda | 4,000 |
| Teteks | Tetovo | AMS Sportski Centar Tetovo | 2,000 |
| Tikvesh 1 | Kavadarci | Gradski Stadion Kavadarci | 7,500 |
| Horizont Turnovo | Turnovo | Stadion Kukush | 1,500 |
| Velazerimi 77 | Kichevo | Velazerimi Arena | 3,000 |
| Vardar Negotino | Negotino | Gradski stadion Negotino | 1,500 |
Shkupi won 7–2 on aggregate.
| Rank | Player | Club | Goals |
|---|---|---|---|
| 1 |  Zoran Baldovaliev | Ak. Pandev | 20 |
| 2 | Dario Desnic | Skopje | 12 |
| 3 | Ljupcho Doriev | Ak. Pandev | 11 |
| Andrian Chavoli | Euromilk GL | ||
| 5 | Jani Atanasov | Ak. Pandev | 9 |
| Sasko Pandev | Ak. Pandev | ||
| Aleksandar Nedanoski | Novaci | ||
| Blagoja Naumoski | Novaci | ||
| 9 | Naumce Bakraceski | Tikves | 7 |
| Mario Krstovski | Horizont Turnovo | ||