The Embry-Riddle baseball team captured its third conference regular season championship in the spring of 1999. That season the Blue and Gold also won its first-ever NAIA Regional title, earning the program's first trip to the NAIA World Series.
 
The Eagles hit .357 as a team that season, outscoring their opponents 501-198. ERAU totaled 127 doubles, 23 triples, 43 home runs, and stole 133 bases in 167 attempts. The pitching staff compiled a 3.12 ERA with 443 strikeouts in 442 innings of work, including a program-record 20 complete games, 11 of which were shutouts.
 
Individually, Luke Martin anchored the pitching staff, going 9-2 with a 2.14 ERA and 151 strikeouts in 117.2 innings pitched with seven complete games and three shutouts, to go along with four saves. Martin also set the single-season program record with a .440 batting average, going 33-for-75. Daniel Calverley led the offense with 83 hits, hitting .401 with 16 doubles, eight home runs, and a team-best 66 RBIs. Bryan Carter batted .373 with a team-high 78 runs scored and a team-leading 29 steals in 36 tries, while Brent McMurtrie hit .369 with a team-best 19 doubles, seven home runs, and 59 runs batted in.
 
Martin was named the Florida Sun Conference Player of the Year and an NAIA First Team All-American. Calverley was named an NAIA Second Team All-American and became the school's first NAIA World Series All-Tournament Team selection. Carter and Greg Coleman both received NAIA All-America Honorable Mention, while Greg Guilliams was named the Regional Coach of the Year for the second time in his career.
 
ERAU got off to strong start that season, winning seven its first eight contests. In fact, the Blue and Gold had a 35-4 record at one point, before dropping four of its final seven regular season games to finish the regular season 38-8-1. The Eagles also opened the season nearly unbeatable in FSC play, winning their first 12 conference games and not suffering a defeat in league play until April 10. Embry-Riddle finished the year 21-2-1 in league play, capturing their third FSC regular season crown.
 
At the FSC Tournament, Embry-Riddle knocked off Nova Southeastern and Flagler before falling to St. Thomas and Northwood to bow out of the tournament. The Eagles would exact some revenge on the Bobcats the following week as ERAU went 4-0 at the NAIA Southeast Regional, including a 2-1 win over STU, to capture the first regional championship in program history.
 
At the World Series, ERAU was downed by Birmingham-Southern, 7-3, before Indiana Tech defeated the Eagles, 9-8, eliminating Embry-Riddle from the tournament.
 
A number of records were set during the 1999 season, headlined by that season being the first and only season to feature multiple no-hitters. Matt Hanson tossed a seven-inning no-hitter in a 6-0 win over Webber College (now Webber International) in the second game of a doubleheader on Feb. 27, allowing just one walk while striking out nine. Almost a month later on March 26, Martin threw the first and only perfect game in program history in a 4-0 win over Mount Vernon Nazarene. Martin picked up nine strikeouts in the seven-inning outing. Martin also tied the program's single-game strikeouts record with 15 in a 15-2 win at Florida Memorial on April 2.
 
Offensively, Calverley set the school record for the longest hitting streak at 29 games, stretching from March 17-May 25, 1999, while Joe Estep established the program record for longest streak of reaching base at 42 games from Jan. 29-April 10, 1999. Also, Carter tied the single-game RBIs record with eight in a 33-0 five-inning win over Clearwater Christian on March 2, as well as tying the program's single-season record for runs scored with 78.