Yes, you can use pedestrian for animals and it has nothing to do with its origin. (for the same sense as a human pedestrian). Though, you have to mention "animal" or the name of the animal along with "pedestrian", otherwise "pedestrian" itself would be understood as a human pedestrian by default.
Keeping the Streets Safe for Animal Pedestrians
It seemed that in the rural highlands of Scotland, cars certainly had the right-of-way over pedestrians, and animal pedestrians at that!
The Countess of Erroll By Ed. D Edwards, S. Elizabeth Edwards
There is also the usage of pedestrian in biology to define animals that walk on foot.
These rules refer, of course, to pedestrian animals, not flying animals or climbing animals. The human animal is a pedestrian, although he is descended from arboreal primates and has some climbing ability.
The Ecological Approach To Visual Perception By James J. Gibson 
Studying the locomotion of aquatic pedestrian animals will contribute to our ideas about possible constraints on a amphibious lifestyle, and the evolutionary transition between aquatic and terrestrial environments.
Issues for Aquatic Pedestrian Locomotion - Marlene M. Martinez