The August survey will determine the number of citizens who do not identify as either male or female.
Intersex people in Kenya often face violence and discrimination.
There are thought to be more than 700,000 of them out of a general population of 49 million.
"Getting information about intersex people in the census will help people understand the challenges we go through," Ryan Muiruri, founder of the Intersex Persons Society of Kenya (IPSK), said he welcomed the government's decision.
"Being included in the census is a big achievement for us," he told the BBC.
South Africa was the first African country to explicitly include intersex people in anti-discrimination law.
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