The president - who is on his first official trip since assuming the largely ceremonial office last month - visited a relief camp in Naroda Patia.
He gave instructions to a local official there to help the victims of the violence, and to allow the immediate admission of children in the camp to school.
Naroda Patia was one of the area worst hit by the rioting, with 82 Muslims burnt alive.
President Kalam's tour comes a day after India's election chief strongly criticised local officials for playing down the scale of the violence, which started after an attack on a train carrying Hindu activists in February.
More than 1,000 people, mainly Muslims, were killed in the subsequent riots which broke out across Gujarat.
Refugees
President Kalam will not be visiting the main refugee camp - the Shah Alam - where thousands of Muslims displaced by the violence are living in squalid conditions.
Reports say local officials have been busy sprucing up those areas that the president is due to visit - including removing rubble and painting houses.
The visit by the president - who has a reputation as a maverick - is adding to the embarrassment for the government which has been insisting that life in the state has returned to normal.
A spokesman for the governing Bharatiya Janata Party (BJP) criticised remarks made by the chief election commissioner on the rehabilitation of riot victims.
"The relief commissioners must do their job and the Election Commission its own," the spokesman, Arun Jaitley, was quoted as saying by The Times of India.
"The job of the Election Commission is to conduct elections."
The BJP is preparing for elections to the Gujarat state assembly and wants the election commissioner to hold the polls immediately.
Opposition parties and civil rights activists say the state is not ready for fresh elections and Muslims still feel insecure.
Analysts say by holding snap elections, Gujarat Chief Minister Narendra Modi and the BJP expect to return to power on a wave of Hindu support.