| 2016-12-31 | BoltonvScunthorpeLeague One · England | 2–1 | League One · England |
| 2016-12-26 | BoltonvShrewsburyLeague One · England | 2–1 | League One · England |
| 2016-12-17 | ChesterfieldvBoltonLeague One · England | 1–0 | League One · England |
| 2016-12-12 | BoltonvGillinghamLeague One · England | 4–0 | League One · England |
| 2016-11-26 | NorthamptonvBoltonLeague One · England | 0–1 | League One · England |
| 2016-11-22 | BoltonvCoventryLeague One · England | 1–0 | League One · England |
| 2016-11-19 | BoltonvMillwallLeague One · England | 2–0 | League One · England |
| 2016-11-13 | PeterborovBoltonLeague One · England | 1–0 | League One · England |
| 2016-10-29 | BoltonvPort ValeLeague One · England | 3–1 | League One · England |
| 2016-10-24 | BuryvBoltonLeague One · England | 0–2 | League One · England |
| 2016-10-18 | MillwallvBoltonLeague One · England | 0–2 | League One · England |
| 2016-10-15 | BoltonvOldhamLeague One · England | 2–0 | League One · England |
| 2016-10-08 | SwindonvBoltonLeague One · England | 0–1 | League One · England |
| 2016-10-01 | BoltonvOxfordLeague One · England | 0–2 | League One · England |
| 2016-09-27 | RochdalevBoltonLeague One · England | 1–0 | League One · England |
| 2016-09-24 | BoltonvBradfordLeague One · England | 0–0 | League One · England |
| 2016-09-17 | WalsallvBoltonLeague One · England | 1–0 | League One · England |
| 2016-09-10 | BoltonvMilton Keynes DonsLeague One · England | 1–1 | League One · England |
| 2016-09-03 | BoltonvSouthendLeague One · England | 1–1 | League One · England |
| 2016-08-27 | CharltonvBoltonLeague One · England | 1–1 | League One · England |
| 2016-08-20 | BoltonvFleetwood TownLeague One · England | 2–1 | League One · England |
| 2016-08-17 | Bristol RvsvBoltonLeague One · England | 1–2 | League One · England |
| 2016-08-13 | AFC WimbledonvBoltonLeague One · England | 1–2 | League One · England |
| 2016-08-06 | BoltonvSheffield UnitedLeague One · England | 1–0 | League One · England |
| 2016-05-07 | FulhamvBoltonChampionship · England | 1–0 | Championship · England |
| 2016-04-30 | BoltonvHullChampionship · England | 1–0 | Championship · England |
| 2016-04-23 | CardiffvBoltonChampionship · England | 2–1 | Championship · England |
| 2016-04-19 | BoltonvCharltonChampionship · England | 0–0 | Championship · England |
| 2016-04-16 | BoltonvMiddlesbroughChampionship · England | 1–2 | Championship · England |
| 2016-04-09 | DerbyvBoltonChampionship · England | 4–1 | Championship · England |
| 2016-04-05 | BrentfordvBoltonChampionship · England | 3–1 | Championship · England |
| 2016-04-02 | BoltonvReadingChampionship · England | 0–1 | Championship · England |
| 2016-03-19 | Bristol CityvBoltonChampionship · England | 6–0 | Championship · England |
| 2016-03-12 | BoltonvPrestonChampionship · England | 1–2 | Championship · England |
| 2016-03-08 | BoltonvIpswichChampionship · England | 2–2 | Championship · England |
| 2016-03-05 | LeedsvBoltonChampionship · England | 2–1 | Championship · England |
| 2016-02-27 | BoltonvBurnleyChampionship · England | 1–2 | Championship · England |
| 2016-02-23 | BirminghamvBoltonChampionship · England | 1–0 | Championship · England |
| 2016-02-20 | BoltonvQPRChampionship · England | 1–1 | Championship · England |
| 2016-02-13 | BrightonvBoltonChampionship · England | 3–2 | Championship · England |
| 2016-02-06 | BoltonvRotherhamChampionship · England | 2–1 | Championship · England |
| 2016-02-02 | WolvesvBoltonChampionship · England | 2–2 | Championship · England |
| 2016-01-23 | BoltonvMilton Keynes DonsChampionship · England | 3–1 | Championship · England |
| 2016-01-16 | Nott'm ForestvBoltonChampionship · England | 3–0 | Championship · England |
| 2016-01-12 | Sheffield WedsvBoltonChampionship · England | 3–2 | Championship · England |
| 2016-01-02 | BoltonvHuddersfieldChampionship · England | 0–2 | Championship · England |