Beijing seeks to tackle worsening congestion and reduce subsidies for transport.
This price rise is the first in seven years, with Beijing ending the practice of a flat 2 yuan ($0.32) fare for all trips.
Students and smart card holders will get discounts.
The new and extended lines are part of a plan to extend the network to more than 600 km (373 miles) by 2016, from around 500 km (310 miles).
The price hike has prompted anger from some commuters, who have taken to social media to complain it will do little to alleviate chronic overcrowding on some lines. Fights occasionally break out as people struggle to make their way onto and off trains at rush hour.
The number of people using Beijing's subway was 3.2 billion last year, up 350 percent from 2007.
Despite the fare increase, the Beijing government will still finance 50 percent of subway operation costs and 62 percent of bus operation costs, state media has reported.