在这部妖怪手表：诞生的秘密喵动画片中,某晚景太正睡觉时，手上的妖怪手錶突然发出刺眼光芒，接着消失不见了！翌日超巨大猫型妖怪「巨大喵」出现，声称世界即将落入魔爪之中并向景太救助。为了找寻线索，景太与威斯帕及地缚喵前往嫲嫲位于毛马本村的家，遇上了神秘的「浮游喵」！他们跟着「浮游喵」一起进行时光旅行，回到了六十年前的世界进行大冒险。在那裡等待着他们的强大敌人究竟是谁？他们又能否顺利找回妖怪手錶？
When the evil Yo-Kai Kin, Gin, and Do steal the Yo-Kai Watch from Keita one night so they can help their master Tokio Ubaune prevent humans and Yo-Kai from being friends, Keita finds help in the Yo-Kai Fuyunyan, who takes Keita, Whisper, and Jibanyan back in time 60 years to when the Yo-Kai Watch was first invented by Keita's own grandfather Keizo while he was a boy. Together, the two boys fight Tokio Ubaune and her evil Kaima Yo-Kai minions to save the world from her evil plans.
