Police were called out to the blast at a property at Nytorgsgatan on Södermalm island at 2.19am. The island is often referred to as Stockholm's “hipster area” and is home to a number of restaurants and shops.
The bomb squad and forensic teams were at the scene on Thursday morning. Police said it was not immediately known what had exploded, for example whether it was a gas leak or a deliberate act.
No one was injured, but the explosion caused damages to the building and windows.
Police did not order an evacuation of the apartment building.
Police were also called out to two other explosions on the same night, one outside a folk museum on Vaxholm in the archipelago and one at a party venue near a Syrian-Orthodox church in Södertälje.
No one was injured in either blast.
Police said on Thursday afternoon that they were investigating the blasts as separate incidents.