Mr Naidu, who is a Rajya Sabha member, arrived at around 10:05 am, five minutes after the voting begun.
The former BJP leader, whose victory appears to be certain, was greeted by members of his party and the opposition.
Congress vice president Rahul Gandhi, his party MPs Jyotiraditya Scindia, Deepender Singh Hooda, Sushmita Dev also cast their votes to elect the next chairman of the Rajya Sabha.
Boxer Mary Kom, a nominated member of the Upper House, and Goa Chief Minister Manohar Parrikar, who is still a member of the Rajya Sabha, also cast their votes.
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