Mr Erdogan, who served three terms as PM, has vowed to give more power to the previously ceremonial post.
Critics of Mr Erdogan say the move will make him more authoritarian. Opposition MPs walked out of the ceremony.
Outgoing Foreign Minister Ahmet Davutoglu is set to be PM after being elected head of the governing AK Party.
Mr Erdogan promised in his presidential oath to protect Turkey's independence and integrity, to honour the constitution and adhere to the principles of the founder of modern Turkey, Mustafa Kemal Ataturk.
Mr Erdogan pledged to safeguard the existence and independence of the 'great Turkish nation' as well as the rule of law, democracy and the secular republic
The new president was treated to full military honours
Opposition MPs walked out of parliament shortly before the swearing-in ceremony
"In my capacity as president of the Republic, I swear upon my honour and repute before the great Turkish nation and before history to safeguard the existence and independence of the state," Mr Erdogan said at the brief ceremony in parliament.
The new president left parliament to lay a wreath at Ataturk's mausoleum in the centre of Ankara - widely regarded as one of the most important symbols of the secular republic.
Another ceremony was held at the presidential palace.
'Deteriorating relations'
MPs from the main opposition party walked out of parliament just before Mr Erdogan arrived, in protest over what they say is his disrespect for the constitution.
Mr Erdogan's family was in parliament to watch the ceremony
The new president left parliament after his swearing-in to lay a wreath at the mausoleum of Mustafa Kemal Ataturk
One legislator was even reported to have hurled a copy of the constitution toward the Speaker, complaining that he was not allowed to express his views.
Main opposition party leader Kemal Kilicdaroglu boycotted the inauguration ceremony.
Under the constitution, Mr Erdogan must cut his ties with the AK Party upon becoming president.
At the party's congress on Wednesday, he said Turkey needed a new constitution, which analysts say would introduce the style of executive presidency that Mr Erdogan openly seeks.
Ahmet Davutoglu is expected to be officially appointed prime minister after the inauguration
Thursday's inauguration ceremony was attended by several heads of state.
However, the US only sent a representative of its embassy and no Western European leader was there.
The BBC's Mark Lowen in Ankara says it is perhaps a sign that Turkey's relations with the West have deteriorated in the past few years of Mr Erdogan's premiership.
Mr Erdogan clamped down violently on anti-government protests last year and recently compared Israel's policy in Gaza to "genocide... reminiscent of the Holocaust".
His supporters say he has transformed Turkey's economy and given a political voice to the country's conservatives.
However, his critics accuse him of having an abrasive style and Islamist leanings.
Our correspondent says Mr Erdogan will face pressure to try to unite a polarised country, which stands on the edge of a volatile Middle East.
Mr Erdogan won the presidential election earlier this month after gaining nearly 52% of the votes in the first round.
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