Flint the Time Detective(1998)

Jikuu Tantei Genshi-kun

It is the 25th century. The dark lord has 'infected' history with time-devices that could damage history beyond repair. Flint and his father lived in the prehistorics when they got turned into fossils. They are discovered and Flint gets turned back to his original state. With the help of his father, a boy Tony and a girl Sara he has to travel through time to bring the time-devices back to the land of time so history will be saved.

(Source: Anime News Network)