The 1999–2000 season was the 89th season in Hajduk Split’s history and their ninetieth in the Prva HNL. Their 3rd place finish in the 1998–99 season meant it was their 9th successive season playing in the Prva HNL.

Updated to games played on 13 May 2000.
Source: rsssf.com
Rules for classification: 1st points; 2nd goal difference; 3rd goals scored
For deciding champions, qualification to UEFA competitions and relegation: 1st points; 2nd head-to-head points; 3rd head-to-head goal difference; 4th head-to-head away goals scored
(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.

Last updated: 13 May 2000.
Source: Sportnet.hr

Ground: A = Away; H = Home. Result: D = Draw; L = Loss; W = Win; P = Postponed.

Source: 1999–2000 Croatian First Football League article

Source: hajduk.hr

Source: Competitive matches

1. Match as awarded to Hrvatski Dragovoljac because was Hajduk fielded suspended player.

2. Match abandoned after 81 minutes due to crowd trouble. Due this the match was awarded to Šibenik.

3. Match abandoned after 86 minutes due to mass fight between both clubs' supporters and the police. The match was a registered with 2:0 Hajduk's win and the club was punished by having their three matches behind closed doors.

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