The former investment banker had never contested an election before and only formed his centrist political movement a year ago.
Mr Macron takes over from outgoing President Francois Hollande.
Hundreds of extra police will be on patrol across the French capital while the ceremony is conducted at the Elysee Palace, the president's official residence.
France has been under a state of emergency since terror attacks in 2015 and a large section of the city centre will be closed to traffic all morning.
Following the handover of power, an inspection of troops will be followed by a 21-gun salute.
Mr Macron will then visit the Arc de Triomphe and lay flowers at the tomb of the unknown soldier.
Emmanuel Macron's task is to bring about the renewal he's promised for France, to shake up its old political order, reinvigorate its anaemic economy and bring down unemployment rates, hovering at around 10%.
To achieve all that Mr Macron needs his brand new political party, La Republique En Marche, to secure a large number of seats in next month's parliamentary elections. Otherwise he will find it hard to push through his planned reforms.
If he fails, he knows he could wind up like his predecessor, the socialist Francois Hollande, who promised to bring change, but ended up being viewed as weak and indecisive, and who leaves office as France's least popular president of modern times.
At 39, Mr Macron will become France's youngest leader since Napoleon and the first to be born after 1958, when France's fifth republic was put in place by President Charles de Gaulle.
His En Marche political movement was formed just last year and as a new party - La Republique En Marche - will be fielding candidates for almost all of France's 577 seats in June's parliamentary elections.
Mr Macron will need a strong presence in parliament to put in place the economic and social reforms he promised voters during his campaign.
He has promised to "work for everyone" and sees his programme as straddling both left and right.
Mr Macron's first week in office will be busy. He heads for Berlin on Monday to meet Chancellor Angela Merkel and to demonstrate his commitment to the European Union.
He is also expected to name a prime minister.
Mr Macron faces major challenges including high unemployment, especially among France's young, and low economic growth.
He says his main aims are to boost investment and to set up a "new growth model" that increases social mobility and helps the environment.
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