The Saddlers are 14th in the table, six points above the relegation zone.
Whitney had been at the Banks’s Stadium for 15 years, joining the club as a physio in 2003.
A club statement read: ‘We thank Jon for his hard work, effort and service during his time at the club but feel that a change in management is in the best interests of the football club at this stage.
‘The club will now go through the necessary recruitment process.’
Ian Sharps has been placed in temporary charge of first-team affairs and will be assisted by John Ward.
Rangers manager Steven Gerrard is weighing up a move for Liverpool full-back Jon Flanagan, reports claim.
Scottish champions Celtic are reportedly ready to offer full-back Calvin Miller a new deal before sending him out on loan.
Everton target Jack Wilshere has sparked a scramble for his signature after confirming he is leaving Arsenal this summer.
Tottenham's hopes of landing Wilfried Zaha have been hit by the news Crystal Palace have offered him a bumper new deal to stay.