In the anime Cosmowarrior Zero, also known as Cosmo Warrior Zero, the version of Harlock that appears is a younger incarnation of the legendary space pirate, depicted at an earlier point in his timeline than in many other works within the creator's broader universe. This Harlock is the captain of a spaceship called the Deathshadow, as his more famous vessel, the Arcadia, is still under construction during the events of this story. He operates in a future where Earth has lost a devastating war against an army of machine men, who now occupy the planet and enforce an uneasy peace.

This younger Harlock is characterized by a fierce and sometimes brutal commitment to his personal code of justice, which prioritizes absolute freedom and resistance against oppressive, totalitarian regimes. He is a stoic, taciturn, and rebellious figure, but in this series, he is also notably more temperamental and aggressive, possessing a shorter fuse than in his older depictions. His driving motivation is to continue fighting against the machine men who have conquered Earth, refusing to accept their dominion even when his own government has capitulated. He is not motivated by wealth but by a deep-seated belief in fighting for what is right, declaring that he fights for something deep in his heart rather than for any external cause or person.

Within the narrative of Cosmowarrior Zero, Harlock serves as a quasi-antagonist and a powerful supporting character, as the story primarily follows Captain Warrius Zero, an Earth fleet captain who is ordered to hunt him down. The uneasy peace that follows the war is threatened by Harlock's continued raids against machine men outposts, which the Earth government fears will provoke their occupiers. This puts him in direct opposition to Zero, a former comrade and a man whom Harlock himself once trained. Key relationships in this series include his deep and loyal friendship with the engineer Tochiro Oyama, for whom he will go to great lengths, and his complex connection with the enigmatic warrior Emeraldas. His interactions with Zero are central, evolving from straightforward adversarial conflict to a grudging mutual respect as Zero comes to understand the purity of Harlock's motives, culminating in the two joining forces against a common, greater threat.

This version of Harlock undergoes notable development, particularly in how his actions affect him on a personal level. While generally ruthless and unwavering in his self-appointed mission, he is shocked to his core when he is tricked into attacking what he believed was a military installation but turns out to be a civilian town. This moment of devastating guilt and shame reveals a vulnerability and a profound sense of honor that tempers his more brutal tendencies. Character development also manifests in his growing, if skeptical, willingness to consider that cooperation between humans and machine men might be possible. In terms of abilities, he is a highly skilled and experienced starship captain and a formidable combatant in personal duels. He is an expert with a saber and possesses deadly accuracy with a gun, able to draw and fire with incredible speed. He is also known for his tactical cunning, though his pride and stubbornness can lead him to deliberately walk into traps, confident in his ability to overcome any challenge.