Mr Fico’s resignation was prompted by the killing of 27-year-old reporter Jan Kuciak, who investigated fraud involving businessmen with political ties.
Her death sparked public anger over corruption and led to the biggest protests in the central European nation since the fall of communism nearly three decades ago.
The murder was similar to that of Maltese investigative journalist, Daphne Galicia, who was murdered with a car bomb last year after investigating corruption among key officials.
The crisis in Slovakia – a member of the European Union, the euro zone and NATO – has tarnished Mr Fico, who has led for 10 of the last 12 years and had sought to stand out from more eurosceptic leaders elsewhere in central Europe.
Facing calls for early elections, the three-party coalition government agreed on Wednesday that Mr Fico would resign, provided that President Andrej Kiska allowed the outgoing prime minister’s Smer party to pick his successor.
Mr Kiska has battled with Mr Fico in the crisis and had urged a government revamp or early election to restore public trust.
Today, Mr Kiska asked Deputy Prime Minister Peter Pellegrini to form a new government.
Fico has tried to keep the coalition government together halfway through its term rather than call early elections, which a junior government party had demanded on Monday.
Slovakia’s economy has grown rapidly in the last decade since he has been in office but many fault Mr Fico for not clamping down harder on corruption and cronyism.
No one has been charged over the killing of Ms Kuciak, who was found shot dead at home with his fiancée in late February.
Following huge anger at the killing of Ms Galicia, Ms Kuciak’s murder has raised more concerns about press freedom within the bloc.
Calling for an urgent inquiry into the deaths MEP Manfred Weber told the EU parliament last week: “We are starting to see new facts emerging. Following Malta following Slovakian, unfortunately two journalists who pressing for freedom of expression have been murdered.”