Manager Dave Jones was given leave from his duties in January to concentrate on clearing his name in connection with child abuse charges, and former England boss Glenn Hoddle was appointed on a temporary basis. Hoddle did well to keep the Saints clear of relegation, and safety was achieved with a 15th-place finish and a respectable 44 points. As the new season approached, it was still unclear as to whether Jones would ever return to the club.

Matt Le Tissier scored a modest six goals during the season, but that was sufficient to bring his total number of Premier League goals to 100, making him the first midfielder to reach this milestone. Le Tissier reached the milestone in Southampton's 2–1 defeat to Sunderland on 1 April 2000 with a goal from the penalty spot.

Updated to games played on 14 May 2000.
Source: Premier League
Rules for classification: 1) points; 2) goal difference; 3) number of goals scored
¹ Chelsea qualified for the UEFA Cup as FA Cup winners

² Leicester City qualified for the UEFA Cup as League Cup winners.
(C) = Champion; (R) = Relegated; (P) = Promoted; (E) = Eliminated; (O) = Play-off winner; (A) = Advances to a further round.
Only applicable when the season is not finished:
(Q) = Qualified to the phase of tournament indicated; (TQ) = Qualified to tournament, but not yet to the particular phase indicated; (RQ) = Qualified to the relegation tournament indicated; (DQ) = Disqualified from tournament.

Source: 1999-2000 FA Premier League table

Source: 11v11.com: 1999-2000 Southampton results
Ground: A = Away; H = Home. Result: D = Draw; L = Loss; W = Win; P = Postponed.

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