The name was changed in late 1882 to Whitby Football Club and continued to play friendly games as well as competing in the Scarborough & East Riding County Cup.
In the non-league system where there is promotion and relegation there is the necessity for those in charge of scheduling matches to move some teams between different regional leagues at the same level to ensure as even a geographical spread as possible.
The 1998-99 FA Cup 3rd qualifying round replay against Bedlington Terriers was a 1–1 draw in regulation time.
The 1999-00 FA Cup 3rd qualifying round replay against Lancaster City was a 2–2 draw in regulation time.
The 2000-01 FA Vase 1 qualifying round replay against Bishop Auckland was a 2–2 draw in regulation time.
The 2005-06 1st qualifying round tie away at Newcastle Blue Star was switched to Whitby.
The 2020―21 FA Cup 1st Qualifying round tie against Warrington Rylands ended 1–1 after regulation time, but Whitby lost the penalty shootout 4–3 During the 2023-24 season the club were docked three points for fielding an ineligible player.