Police say Ellie's body was found in San Jose.
Her mother Chrystal Obi released a statement calling Ellie "the most charming, funny, smart" girl.
"We are heartbroken at the loss of our dear sweet Ellie. She was the most charming, funny, smart, friendly little girl. Ellie loved dancing and meeting new people. She so easily made friends and spread so much joy everywhere she went. She will be remembered for her smart and curious mind, her big smile, and her warm loving heart. Ellie's life was full of so many people who loved her so much and will miss her beyond words can explain. We wanted to extend our thanks to the community at large in their support through the search for Ellie."
Earlier Saturday, Fremont authorities were informed by San Jose police a girl resembling Ellie was located deceased in San Jose.
This remains an active investigation.
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Fremont police looking for missing 3-year-old girl
Authorities say Ellie, who lived with her mom in Mountain View, was last seen Thursday at 6 p.m. with her father at the Casa Arroyo Apartments on Rancho Arroyo Parkway in Fremont.
According to her mother, the 3-year-old was supposed to be returned Friday night per a custody agreement but she was informed that the girl's father was found dead in a nearby city and Ellie was missing.
Ellie's family has set up a GoFundMe to help with her funeral expenses.