"Fairy Princess Minky Momo" centers on Momo, a magical princess from the land of Fenarinarsa, a realm where dreams and fairy tales come to life. Sent to Earth to assist humanity in rediscovering their dreams and hopes, Momo takes on the guise of a young girl living with a kind elderly couple. Her mission is to collect the "Phenomenal Pearls," magical items that will restore her homeland, which has begun to fade due to humanity's growing loss of wonder and imagination.

Momo is accompanied by her three animal companions: Mocha the dog, Pipil the monkey, and Sindbook the bird. Together, they travel across Earth, helping people in need and solving problems through the use of Momo's magical abilities. She can transform into various adult professions, such as a doctor, pilot, or police officer, using her "Minky Rod," a magical wand that grants her the skills and attire necessary for each role. These transformations allow her to address the challenges she encounters while spreading hope and inspiration.

The series is episodic, with each episode presenting a self-contained story where Momo aids individuals facing personal struggles or societal issues. Her interventions often emphasize themes of kindness, perseverance, and the importance of dreams. However, the narrative takes a dramatic turn midway through the series when Momo faces a tragic event, marking a significant shift in tone and adding emotional depth to her journey.

As the story progresses, Momo's connection to humanity deepens, and she grapples with the complexities of her dual identity as both a fairy princess and a human. The series explores her growth as a character, her relationships with those around her, and the broader implications of her mission to restore Fenarinarsa. Through its blend of whimsical fantasy and heartfelt storytelling, "Fairy Princess Minky Momo" presents a tale of hope, resilience, and the enduring power of dreams.