The judge, Marcel Montalvao, issued the order because WhatsApp owner Facebook failed to hand over information requested in a criminal investigation.
WhatsApp was temporarily shut down in December for similar reasons.
The service is widely used in Brazil, where mobile phone owners face some of the highest charges in the world.
The order was due to come into place from 1400 local time (17:00 GMT) and applies to Brazil's five main mobile operators.
A rival service, Telegram, reported a surge of applications after the block came into place.
WhatsApp said it was "disappointed" by the move, saying it had co-operated fully with the local court.
"This decision punishes more than 100 million Brazilians who rely on our service... in order to force us to turn over information we repeatedly said we don't have," a statement said.
In March the same judge ordered the arrest of a Facebook executive based in Brazil for failing to comply with an attempt to block WhatsApp.
He was released the next day.
Source: BBC
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