The Cougars won an unprecedented seventh consecutive Golden State Athletic Conference (GSAC) regular season crown and advanced to their sixth NAIA National Tournament in the past 7 years. They earned the No. 7 seed at the NAIA Championship Tournament and advanced to the NAIA semi-finals for the second straight season, the first program to make it to consecutive NAIA Final Four appearances since Belmont University in 1995 and 1996.

Azusa Pacific posted a 13-2 mark prior to the GSAC opener, The Cougars lost to eventual WAC champ Utah in Salt Lake City. However, they won the Sea Warrior Classic, beating NCAA Division II Hawaii Pacific in the finals, 84-74, for their first win over the Sea Warriors in Honolulu. The following week, the Cougars won the State Farm Holiday Classic at CS Bakersfield, knocking off NCAA Division II North Dakota State in the first round, and CS Bakersfield, 75-68, in the championship game. Azusa Pacific became the first team other than CS Bakersfield to win the tournament, and in the process earned their first-ever victory in Bakersfield. Azusa Pacific annihilated Bethany 120-37, the 83-point margin being the biggest in program history.

The Cougars won their GSAC opener over So. Cal College, before falling 75-66 at Westmont. They won their next 5 games, including one in which they recorded one of the biggest comebacks in program history. Trailing by 20 points on the road at the NAIA's No. 10-ranked Biola, the Cougars rallied to knock off the Eagles and win their fourth straight over Biola. So. Cal College upset the Cougars in the first game of the second half of GSAC play, but the Cougars responded with an 82-79 win over No. 9 Westmont in Azusa that ultimately decided the GSAC title. Biola again fell victim to a Cougar comeback, this one in Azusa, losing to the Cougars 69-61. The Cougars wrapped up their GSAC crown with an 82-55 victory at Fresno Pacific. Holding the No. 1 seed in the GSAC tourney, the Cougars were stunned by Point Loma Nazarene, 78-77, in overtime, costing them the GSAC Tournament Championship and a high seed in the NAIA National Tournament.

Thanks to upsets around the country, the Cougars were given the No. 7 seed at the NAIA Tournament. They opened up with a less than inspiring 75-67 win over Edward Waters College (Fla.). In the second round, the Cougars dominated Findlay (Ohio), ousting the Oilers, 87-68. In the quarterfinals, the Cougars sent No. 2 Union (Tenn.) packing with an 85-77 win that propelled Azusa Pacific into the Final Four for the second straight year. In the semifinals, the Cougars fell to eventual NAIA National Champion Life University (Ga.) 77-71.

Senior point guard T.J. Walker, who averaged 15.8 points, 6.0 rebounds and 5.1 assists and was named 1999 GSAC Player of the Year, was also named NAIA First Team All-American, becoming the first GSAC player ever to earn back-to-back First Team All-American recognition. Junior forward Kevin Daley, who led the Cougars in scoring (16.0 avg.) and rebounding (6.0 avg.) was a 1999 All-GSAC pick and received NAIA Honorable Mention All-American recognition. Junior guard Jerome Joseph, who averaged 15.3 points and 4.5 rebounds, was also a 1999 All-GSAC selection and was an NAIA Honorable Mention All-American while being named to the NAIA All-Tournament Team after scoring 61 points in the 4 tournament games.