Justice League Heroes: The Flash is the Game Boy Advance version of Justice League Heroes released from Xbox and PlayStation 2. This version focuses primarily on The Flash and features 2D sidescrolling action gameplay and a sidestory to the console game's plot.

The Flash responds to a robot invasion in Keystone City, discovering a global crisis orchestrated by an unknown mastermind. Guided by the Justice League via the Watchtower, he defeats Gorilla Grodd, who reveals an alliance with the robots' controller. The Flash then tackles threats in Gotham City, defeating Killer Frost, who is also linked to the conspiracy. Next, he aids Wonder Woman's island, Themyscira, overcoming the sorceress Circe, who names Brainiac as the mastermind behind the diversions. The Flash then confronts Zoom in a flooded city caused by earthquakes, learning Zoom is also working with Brainiac. Finally, in Metropolis, the Flash rescues Superman from Brainiac's ship, defeats Brainiac, and uncovers his plan to build a device around a stolen meteor. This device frees Darkseid from an extradimensional prison, setting the stage for a larger Justice League battle against Darkseid's threat to Earth.