At The Indian High Group of Schools, pupils in the kindergarten and primary sections performed songs and dances. They also dressed in the colours of the flag.
Special performances were planned throughout the day.
"This is a country with rich heritage and culture that communicates so much to the world through its flag," said Punit MK Vasu, chief executive of The Indian High Group of Schools.
"The carefully chosen colours, expressing everything from courage to hope, peace and mental toughness, unity and diversity, manifests the vision of the leadership and the country’s profile in the international community.
"It is the ideal occasion for all of us across the education community to pay respects and tributes to the rulers."
Brighton College Dubai held a ceremony that was broadcast to the school in which the headmaster, Simon Crane, alongside the school's Emirati and UAE ambassadors, spoke about the meaning behind the day.
Pupils at Repton Dubai came together at 11am to raise the flag of the UAE.
Delhi Private School Dubai invited police officers to mark the occasion with them and raise the UAE flag during a ceremony at the school.
Flag Day was first celebrated in 2013.
It is commemorated every year on the anniversary, November 3. It is not a public holiday.