The International Committee of the Red Cross (ICRC) says it expects this number to double by the end of the day.
Government forces, backed by Russian allies, took nearly all remaining rebel-held parts of Aleppo this week after a four-year battle.
It represents a major victory for President Bashar al-Assad.
He hailed the "liberation" of Aleppo and said history was being made.
The evacuation of civilians, rebels and their families had been due to take place on Wednesday but an earlier ceasefire deal collapsed.
It is unclear how many rebels are being evacuated along with civilians. The evacuees are being transferred to rebel-held areas in neighbouring Idlib province.
"This for us is the first step, it was a positive one," Robert Mardini, ICRC regional director for the Near and Middle East, told Reuters news agency in Geneva.
"We were able so far to evacuate 26 wounded persons from east Aleppo and close to 1,000 civilians, who were transferred from east Aleppo to western rural Aleppo."
"Many more" rotations of buses and ambulances would be needed in the coming days, he added.
Syrian state TV had earlier said that "4,000 rebels and their families would be evacuated from eastern districts on Thursday", adding that "all the procedures for their evacuation" were ready.
A statement from the Russian Centre for the Reconciliation of Opposing Sides in Syria, part of Russia's ministry of defence, said the Syrian authorities had guaranteed the safety of all members of the armed groups who decided to leave Aleppo.
Hezbollah, the Lebanese Shia Muslim movement backing the Syrian government, said there had been "big complications" but that "intensive contacts... led to re-consolidating a ceasefire to exit armed fighters from eastern districts".
The rebels confirmed a fresh ceasefire had come into effect at 03:00 GMT and that a new deal had been agreed.
As operations began, an ambulance service official in eastern Aleppo said that one convoy of ambulances had been shot at, with three people injured.
The White Helmets civil defence group tweeted that one senior volunteer had been shot and injured by a sniper while clearing an evacuation route for ambulances.
Where are the evacuees being taken?
Buses and ambulances are taking the injured, civilians and rebel fighters to the neighbouring province of Idlib, most of which is controlled by a powerful rebel alliance that includes the jihadist group Jabhat Fateh al-Sham.
The buses left Aleppo via the road through the government-controlled south-western district of Ramousseh, heading towards the nearby rebel-held towns of Khan Touman and Khan al-Asal.
The chief of the Russian military's General Staff, Gen Valery Gerasimov, told a news briefing: "A humanitarian corridor has been created for the evacuation of militants."
"This corridor is 21km long," he said, adding, "6km lie across Aleppo's territories controlled by government troops and another 15km through territories in the hands of illegal armed groups."
Twenty passenger buses and 10 ambulances were being used for the operation, the general said. Some rebels were using their own vehicles, numbering 100, he said.
Elizabeth Hoff, of the World Health Organization, said the operation was "going smoothly".
How many remain in eastern Aleppo?
The figures vary wildly. Generally it's believed up to 50,000 people remained ahead of the evacuation.
That is said to include about 4,000 fighters and about 10,000 family members of fighters.
However, one Turkish government minister said up to 100,000 people might have to be evacuated.
Aleppo's besieged residents have faced weeks of bombardment and chronic food and fuel shortages.
Medical facilities in the city have largely been reduced to rubble, as rebels have been squeezed into ever-smaller areas by a major government offensive, backed by Russian air power.
Russian Lt Gen Viktor Poznikhir said on Thursday that, with the evacuation, the Syrian armed forces had almost finished their operations in Aleppo.
Why did the earlier deal fail?
Syria's government and its ally Iran had insisted the evacuation from eastern Aleppo could happen only with the simultaneous evacuation of two villages - Foah and Kefraya - being besieged by rebels in north-western Syria.
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- 'The most beautiful city in the world'
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Hours after the first agreement - brokered mainly by Russia and Turkey - collapsed, air strikes resumed.
What will the government do next?
In October, President Assad said victory in Aleppo would be "the springboard... to liberate other areas from terrorists", a term the government uses to describe all rebel fighters.
He singled out Idlib province, west of Aleppo, that is almost entirely controlled by an alliance of Islamist rebel factions and Jabhat Fateh al-Sham, formerly known as al-Nusra Front.
Idlib contains border crossings used by rebels to receive supplies from Turkey, a key backer. It also borders the coastal province of Latakia, the heartland of Mr Assad's minority Alawite sect.
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