ASKY Airlines said it took the decision to keep “its passengers and staff safe during this unsettling time”.
The number of people killed by the virus in West Africa has now reached 672, according to new UN figures.
In Sierra Leone, the doctor who led the fight against Ebola, Sheik Umar Khan, has died of the disease.
Government officials hailed Dr. Sheik Umar Khan, 39, as a “national hero”.
The government disclosed last week that he was being treated for Ebola and had been quarantined.
His death follows that of prominent Liberian doctor Samuel Brisbane at the weekend.
Ebola kills up to 90% of those infected, but patients have a better chance of survival if they receive early treatment.
It spreads through contact with an infected person’s bodily fluids.
The outbreak – the world’s deadliest to date – was first reported in Guinea in February. It then spread to Liberia and Sierra Leone.
ASKY is the second airline, after Nigeria’s largest airline, Arik Air, to ban flights to Liberia and Sierra Leone.
It had not halted flights to Guinea, but passengers departing from there would be “screened for signs of the virus”, ASKY said.
Last week, Nigeria, Africa’s most populous country, reported its first case – that of Liberian finance ministry official Patrick Sawyer who flew to the main city, Lagos, in an ASKY flight.
Liberia has deployed police officers at the international airport in the capital, Monrovia, to ensure passengers are screened for symptoms of Ebola.
“We have a presence of the police at the airport to enforce what we’re doing,” said Binyah Kesselly, chairman of the Liberia Airport Authority.
“So if you have a flight and you are not complying with the rules, we will not allow you to board.”
Most border crossings in Liberia have been closed to contain the outbreak and affected communities are being quarantined.
Liberia has also suspended all football activities in an effort to control the spread of Ebola.
In a statement, the World Health Organization (WHO) said that 1,201 Ebola cases had been reported in Guinea, Liberia and Sierra Leone.
Of the 672 deaths, the highest number was in Guinea with 319, followed by Liberia with 249 and Sierra Leone with 224, it said.
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