Police also chased demonstrators with batons on Wednesday. More than 200 youths threw stones and broken chunks of cement blocks at the walls.
As they scattered and regrouped, more students skipped out of a nearby boys’ school and joined in.
Many shouted "Death to America and Israel" as they ran towards the walls-able only to get within about 60 metres before being blocked by concrete barriers that surround the embassy.
"America is the root of all the problems, and we want this embassy in Bahrain to be shut down," said a teenage boy who identified himself only as Muhsin, a student from a nearby school.
There was no damage to the embassy and no injuries from the clashes.
Two dozen to three dozen riot police in blue camouflage, carrying batons and shields, arrived quickly and began chasing protestors around the outside of the embassy compound. Some of the demonstrators hid their faces behind handkerchiefs.
No arrests were made as the youths charged off well ahead of the police, then circled back to take another run with fresh handfuls of stones.
A police helicopter hovered overhead.
Embassy officials could not immediately be reached for comment.
Traffic police cordoned off roads near the embassy, leading to traffic jams in the residential suburb of Manama where the embassy is located.
Anti-US sentiment has been running high in the Middle East since the assassination of Yasin, Hamas' spiritual leader.