"Bokura wa Tsuyoki na Runner da!" centers on a group of high school students who form a relay team to compete in the prestigious Hakone Ekiden, a long-distance relay race held annually in Japan. The protagonist, Kakeru Yamanobe, is a talented but troubled runner who initially distances himself from team sports due to a past incident involving his former teammates. After being caught shoplifting, Kakeru is coerced into joining Kansei University's track team by Haiji Kiyose, a determined and charismatic senior who dreams of qualifying for the Hakone Ekiden despite the team's lack of experience and resources.

The narrative explores the challenges of building a cohesive team from scratch, as the members come from diverse backgrounds and possess varying levels of running experience. Alongside Kakeru and Haiji, the team includes characters like Prince, a manga enthusiast with no prior running experience; twins Joji and Jota, who bring humor and energy; and Shindo, a disciplined and hardworking athlete. Each member undergoes personal growth as they train rigorously, overcoming physical and emotional hurdles to prepare for the race.

The story delves into themes of perseverance, camaraderie, and self-discovery, highlighting the physical and mental demands of long-distance running. The team's journey is marked by setbacks, rivalries, and moments of triumph, culminating in their participation in the Hakone Ekiden. The race serves as a test of their collective resolve and individual strengths, with the narrative emphasizing the importance of teamwork and mutual support in achieving shared goals. Through its focus on the characters' development and their pursuit of a seemingly impossible dream, the series captures the spirit of determination and the transformative power of sports.