After Sunday's 2-1 loss at Liverpool, Spurs are third-bottom in the WSL, just two points above the relegation zone.
Skinner, 43, took charge in November 2020 following a spell as England's assistant head coach and led Spurs to a fifth-placed finish last season.
Assistant Vicky Jepson will take over the team for Wednesday's WSL game at home to bottom club Leicester City.
