Air space around the airport, which is among the busiest in Scandinavia, was closed while authorities investigated the intrusion.
No planes were allowed to take off or land at Arlanda airport for around 30 minutes.
“Some planes were left stationary while others were circling [above]. We took this very seriously. Drones are a major concern for flight safety,” Åsa Öhman, a press officer at Swedavia, which operates the airport, told Swedish news agency TT.
Arlanda is Sweden's largest airport, offering routes to 172 destinations around the world.
Flights resumed on Monday night and were operating as usual by Tuesday morning, while police continued to investigate the incident.
According to Swedish law, a permit is required to operate a drone, with extra paperwork needed in order to enter controlled flying zones, such as that over Arlanda airport.
It is not the first time that a drone has caused chaos in Swedish airspace.
Earlier this month a small civilian drone on entered the Stockholm airspace, forcing authorities to briefly halt all commercial traffic at the city’s smaller Bromma airport.
The airport reported that it was the third time that a tiny remote-controlled aircraft had prompted officials to ground flights.