The 2016–17 season was Charlton Athletic's 95th season in their existence and first back in League One – since being champions in 2011–12 – following relegation from the championship the previous season. Along with competing in the League One, the club also participated in the FA Cup, League Cup and League Trophy. The season covered the period from 1 July 2016 to 30 June 2017.
^Foley was born in Luton, England, but also qualified to represent the Republic of Ireland internationally through his parents and represented them at U-21 and B level before making his international debut for the Republic of Ireland in May 2009.
^Chicksen was born in Milton Keynes, England, but also qualified to represent Zimbabwe internationally through his father and would make his international debut for Zimbabwe in March 2018.
^Crofts was born in Chatham, England, but also qualified to represent Wales internationally through a grandparent and represented them at U-19 and U-21 level before making his international debut for Wales in October 2005.
^Fox was born in Chelmsford, England, but also qualified to represent Wales internationally and represented them at U-21 level.
^Kashi was born in Aubervilliers, France, but also qualified to represent Algeria internationally and made his international debut for Algeria in January 2015.
^Ansah was born in Bexley, England, and represented them at U-16 and U-17 level, but also qualified to represent Ghana internationally and has confirmed his international allegiance to them.
^Harriott was born in Croydon, England, and represented them at U-19 level, but also qualified to represent Guyana and Jamaica internationally and would make his international debut for Guyana in March 2019.
^Bergdich was born in Compiègne, France, but also qualified to represent Morocco internationally and represented them at U-23 level before making his international debut for Morocco in 2012.
^Vetokele was born in Ostend, Belgium, and represented them at U-17, U-18, U-19, and U-21 level, but also qualified to represent Angola internationally and made his international debut for Angola in 2014.