The explosions happened at two busy areas on the outskirts of the city as people were heading to work.
Israeli media said the teenager who died was an IsraeliCanadian religious student named Aryeh Shtsupak.
Israel's internal security minister said at one scene that this was "an attack we haven't seen in a long time".
The atmosphere in the city feels volatile in a year of intensifying violence: Palestinian gun and knife attacks have targeted Israelis, and Israeli military raids have killed Palestinian gunmen and civilians in the occupied West Bank.
A return to the use of explosives in Jerusalem makes it one of the most significant attacks of its kind in years.
No group has so far said it was behind the blasts. However, the Palestinian militant groups Hamas and Islamic Jihad both praised the perpetrators of what they referred to as the "operation".
The first explosion happened in Givat Shaul, close to the main entrance to Jerusalem, just after 07:00 (05:00 GMT) on Wednesday.
Israeli medics said the blast wounded 12 people, including the teenage boy who died later at the Shaare Zedek Medical Center.
About 30 minutes later, there was a second blast in Ramot Junction, another entrance to the city. It left three people with minor injuries.
At the scene of the first explosion, the pavement was scattered with debris. Masked Israeli security forces sealed off the site, while the pieces of a badly damaged bicycle were put into forensics bags.
One man from a Jewish ultra-Orthodox neighbourhood opposite told the BBC that he was woken as his building shook. Many of those waiting for buses were apparently from the community.
A small protest was also taking place with a sign held by young Israeli men calling for "revenge".
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