Mr Zapata, 40, took off from Sangatte, near Calais, at 06:17 GMT on Sunday and landed in St Margaret's Bay in Dover.
The invention, powered by a kerosene-filled backpack, made the 22-mile (35.4-km) journey in 22 minutes.
Mr Zapata, a former jet-ski champion, had failed in his first attempt to cross the Channel on 25 July after complications with refuelling.
"We made a machine three years ago... and now we've crossed the Channel, it's crazy," he told reporters, before breaking into tears.
"Whether this is a historic event or not, I'm not the one to decide that, time will tell," he added.
Mr Zapata told crowds in Dover that he had reached speeds of up to 170km/h (106mph) during the flight.
His greatest challenge had been to refuel by switching to another backpack during the crossing.
In his previous attempt, the Frenchman fell into the sea before reaching a boat that was carrying a second backpack.
A larger boat and platform was used for this latest crossing, with an escort by three helicopters.
Mr Zapata received widespread attention during the annual Bastille Day parade in Paris last month, when he took part in a military display on his futuristic flyboard.
France's military has also sought to develop the technology for itself, and recently gave his company, Z-AIR, a €1.3m ($1.4m; £1.28m) grant.
In an interview with France Inter radio, French Defence Minister Florence Parly said the flyboard could serve several purposes, "for example as a flying logistical platform or, indeed, as an assault platform".