Fighter jets flew overhead and there was a 21-gun salute as Mr Sisi took his oath in parliament.
Mr Sisi won 97% of the vote in March but on a turnout of just 41% and with his only opponent a Sisi supporter.
Supporters say he has brought much-needed stability, opponents that he has stifled democracy with arrests.
Egyptian air force fighter planes flew overhead releasing smoke in the colours of the national flag as Mr Sisi, 63, approached parliament in his motorcade.
After taking the oath of office he said in his speech he wanted to create a “common space” for Egyptians and that only those “who chose violence, terrorism and extremist thought as a way to impose their will” would be excluded.