The FSA's move into Syria was made the previous week and "aimed to unite all rebel groups", Brig Gen Mustafa al-Sheikh of the FSA's military council told the Associated Press news agency.
In the video which appears to show him announcing the move, Gen Asaad says the FSA will fight "side by side" with "all brigades and factions" until victory.
Gen Asaad adds the capital Damascus "will be liberated soon, God willing" but also rejects the idea that the FSA is seeking to replace the current regime.
The Syrian people must agree on any new government, he says.
The move is significant as the FSA has previously been criticised for leading from Turkey and being out of touch with realities on the ground, the BBC's Jim Muir in Beirut reports.
It now seems the FSA has territory it feels is reliably under their control, he adds.
The new command centre, in a secret location, will clearly be highly vulnerable to air attack by the regime - something that could increase pressure for some kind of international air cover for the "liberated areas", our correspondent says.
Meanwhile, in the northern Syrian city of Aleppo, a government offensive against districts where rebels have been operating has reportedly been continuing.
Graphic footage posted online on Saturday appears to show the aftermath of an airstrike in the Al-Missar quarter of the city.
Residents are shown trying to pull dead bodies from the rubble, including those of two young children.
The UK-based opposition group the Syrian Observatory for Human Rights said at least five people had died in a strike in Al-Missar.
Fighting was also reported by the Observatory between rebels and government forces in the western part of Aleppo province.
The city has been the scene of rebel activity and heavy government bombardment for weeks.
The Local Co-ordination Committees (LCC), a network of anti-government activists based inside Syria, said 45 people had been killed in and around Damascus on Saturday, where clashes between rebels and government forces have also been raging in recent weeks.
The LCC put the toll in Aleppo on Saturday at 33.
Also on Saturday, the Lebanese military said FSA rebels had attacked a Lebanese army border post near the town of Arsal.
The Lebanese army said in a statement that this was the second time in less than a week that the FSA had infiltrated Lebanese territory. Military reinforcements have now been moved to the area.
Source: BBC News