"Cheer Boys!!" centers on Haruki Bandou, a former judo athlete who, after quitting the sport due to a lack of passion, finds himself searching for a new purpose. Encouraged by his childhood friend Kazuma Hashimoto, Haruki joins a fledgling all-male cheerleading team at Meishi University. The team, initially formed as a joke, gradually evolves into a serious endeavor as the members discover their shared passion for cheerleading and the camaraderie it fosters.

The narrative explores the challenges of building a cheerleading squad from scratch, highlighting the struggles of recruiting members, overcoming societal stereotypes about male cheerleaders, and mastering the physical and technical demands of the sport. The team, named Breakers, faces internal conflicts, personal insecurities, and external skepticism, but their determination to prove themselves drives them forward. Key characters include Kazuma, the enthusiastic and optimistic co-founder of the team; Wataru Mizoguchi, a reserved and disciplined member with a background in gymnastics; and Shou Tokugawa, a former rugby player who brings strength and leadership to the group.

As the Breakers grow, they participate in competitions, learning to synchronize their movements, build trust, and perform as a cohesive unit. The series delves into the personal growth of each member, showcasing how cheerleading helps them confront their fears, build confidence, and form lasting bonds. The story balances lighthearted moments with emotional depth, emphasizing themes of perseverance, teamwork, and self-discovery. Through their journey, the Breakers challenge societal norms and inspire others to pursue their passions, regardless of gender or preconceived expectations.