The body of Flaihan, al-Hariri's close aide and one of the architects of his economic policies, was flown to Beirut on Thursday night from France where he died from serious burns suffered in the 14 February bombing.
The cortege - led by government ministers, ministers of parliament and al-Hariri's son and heir Saad al-Din - set out from the al-Hariri family residence to the nearby home of the slain minister.
A funeral was to be held at a Protestant church in the city centre before the burial.
Flaihan, 42, died on Monday in a military hospital near Paris where he had been taken immediately after the bombing.
His death brought the toll from the blast to 20.
Tent set up
A tent had been set up in the central Martyrs' Square for prayers for Flaihan, a Protestant MP from al-Hariri's parliamentary bloc who served as economy and trade minister between 2000 and 2004.
US-educated, with an MA from Yale University and a PhD in economics from Columbia University, Flaihan worked for the World Bank and the UN Development Programme before launching his political career in 2000 when he was elected to parliament.
He is survived by his wife, Yasma, and two young children.