The President Hassan Rouhani-led Iranian government hopes the move will strengthen the country's economy, battered by western sanctions.
Though petrol in Iran is still among the cheapest in the world, analysts say the latest price rise will be unwelcome in a country where a quarter of adults are jobless or under-employed.
The subsidies have been blamed for making petrol cheaper than bottled mineral water.
The cost of subsidised petrol, available in limited amount to each motorist, rose from about $0.16 a litre to $0.28 a litre at midnight.
"We have been preparing for two months to implement these plans in provinces, cities and rural areas," Interior Minister Abdolreza Rahmani Fazli told state media.
This year Iranians have also witnessed their electricity bills go up by 24 percent and those for water by 20 percent.