Police were on maximum alert to prevent the outbreak of violence during the protest. Most of the protestors were young men, local reports said.
The president's opponents had hoped for a crowd of at least 50,000 to help pressure her to resign. Some opposition politicians had predicted a gathering of 1 million, the Philippine Star reported.
Arroyo has ignored calls for her resignation over charges of election fraud, even after 10 Cabinet members resigned last week.
Two of Arroyo's predecessors were ousted by "people power" movements, backed by religious leaders and the military. Both groups have declined to back the current revolt, however.
Catholic bishops have called for a truth commission to investigate charges against her, and the army has declared it will remain neutral.