The two first met when Ezra was sneaking around in the Ghost near Kanan's room. Though Chopper barely knew him, he seemed to agree with Hera to go rescue him when he was captured by the Empire. Chopper loves to play pranks on both Ezra and Zeb forming a rivalry between them. Though, overtime, it is shown the two slowly formed a friendship, as they were trying to rescue Kanan and Chopper went along with his plan and Ezra having faith in him that he will succeed in his part of the mission. Since that mission, Ezra and Chopper's friendship has grown more, as Chopper was worried about Ezra when he started to wonder who he should really be. When Ezra found out his parent had died during an escape attempt in an Imperial prison, Chopper comforted Ezra along with Kanan.
Chopper also begrudgingly follows Ezra's orders ("Steps Into Shadow") and follows him to Tatooine when Ezra sneaks off of the base, chosing to follow him in the desert rather than look for civilization.