What are the causes of a foot to feel like you are walking on pebbles in your shoe?

Possible: Neuroma or neuropathy.

Metatarsalgia: The sensation of walking on pebbles is called metatarsalgia . It can be causing by a "dropped" or prominent metatarsal head often due to hammered or clawtoes . People suffering from rheumatoid arthritis or aging may have a migration of the fat pad under the metatarsal heads also leading to metatarsalgia.