Anne Hidalgo said they will be given the Medal of the City of Paris.
She told the French sports newspaper L'Équipe they had distinguished themselves by the "atmosphere" they created at the tournament in France.
The medal - known as the Grand Vermeil - is regarded as Paris's most prestigious honour and has been awarded to a wide variety of cultural and political figures.
Ms Hidalgo has written to Irish President Michael D Higgins to tell him of the award, but it is not yet known when the ceremony to present the medal will take place.
I believe that the awarding of a medal to football fans for quality behaviour and good humour is unique and I am delighted for them. I can only imagine what kind of a party they are going to have after the presentation for the craic will be mighty!
Northern Ireland’s fans also made a big impression on the French at Euro 2016 — and now Paris is going to say “merci”.
The city’s mayor Anne Hidalgo said she would be giving supporters from both sides of the border an honorary medal for their fantastic behaviour.
Further adding that “The supporters from Ireland and Northern Ireland distinguished themselves by their exemplary attitude, fair play and good mood”