PBA was the vision of and was founded by Jess C. Moody in 1968 while he was the pastor of First Baptist Church of West Palm Beach.

He resigned from PBA in 2002 to accept a position as Assistant Attorney General for Administration with the United States Department of Justice.

President Clark announced his retirement from PBA during the 2008–2009 academic year at the end of June.

A team of health alert nurses at PBA would text any COVID-positive students to stay home, then commence contact tracing.

The campus, located between I-95 and Parker Avenue just north of Southern Boulevard, provides PBA facilities for training and hosting intercollegiate and intramural and club sport competitions.

[12] Over the past several years, PBA has experienced unprecedented growth on its West Palm Beach campus.

He filed a discrimination complaint with EEOC with hopes to establish adequate academic freedom for PBA faculty.

In a letter to PBA president Debra Schwinn, AAUP Senior Program Officer Michael DeCesare wrote that Joeckel "was abruptly terminated prior to the end of (PBA's) term after complaints were made regarding his teaching a unit on racial justice... We hope you appreciate that if allegations against faculty members were commonly handled in this manner at Palm Beach Atlantic University, academic freedom and due process would have little meaning.

"[21] The Foundation for Individual Rights in Education (FIRE) issued a faculty letter condemning PBA's decision and supporting Joeckel.

The letter stated, "We are deeply concerned about the state of academic freedom at Palm Beach Atlantic University after PBA fired English professor Samuel Joeckel because material in the racial justice unit of his composition course was deemed to be 'indoctrinating students.'"

The letter continues, "We join FIRE in condemning Palm Beach Atlantic’s choice not to renew Joeckel’s contract, a decision which violated Joeckel’s rights and casts an impermissible chilling effect over other professors who may fear that teaching controversial material could jeopardize their jobs.

We urge Palm Beach Atlantic to reaffirm its commitment to academic freedom and to pledge that it will refrain from retaliation against professors for their protected expression."

[22] Like the AAUP, FIRE wrote a letter to PBA and "urged the university to reaffirm its commitment to academic freedom and renew professor Joeckel’s contract."

PBA mission teams travel to countries all over the world and minister through evangelism, performing arts, street ministries, construction, medical outreach, sports workshops and more.

PBA is a member of the NCAA Division II ranks, primarily competing in the Sunshine State Conference (SSC) since the 2015–2016 academic year as a provisional member for most their sports (achieving D-II full member status in 2016–2017);[29][30] while PBA's men's and women's track & field teams compete as NCAA D-II Independents as the conference does not sponsor these sports.

PBA competes in 18 intercollegiate varsity sports: PBA men's sports include baseball, basketball, cross country, golf, lacrosse, soccer, tennis and track & field; while PBA women's sports include basketball, beach volleyball, cross country, golf, lacrosse, soccer, softball, tennis, track & field and volleyball.

PBA's Marshall and Vera Lea Rinker Athletic Campus has beach volleyball, soccer, lacrosse, baseball, softball, tennis, and running trails as well as a new state of the art weight and training rooms.

[31] The sailfish is a predatory billfish, distinguished by its prominent dorsal fin and ability to accelerate to speeds unmatched by any other fish, up to 68 mph.

[32] The sailfish can achieve these speeds and jumping heights as it leaps from the ocean, as one of the fiercest marine predators.

The sailfish’s speed, power, and prominence along Florida’s Atlantic coast made it a natural choice for PBA's mascot.