The firm, which has serviced London City Airport in Docklands for the past 22 years, will team up with the East End event space in its most successful year to date.
CityJet’s executive chairman Pat Byrne said the deal was “very practical and very important” while Excel CEO David Pegler called the co-branding “really exciting”.
Sales and marketing initiatives will offer clients, exhibitors and visitors using the 100,000 sqm space the chance to benefit from competitive air pricing on CityFlex and CityPremium fare classes.
Mr Byrne said the airline would be able to arrange charter flights to City Airport for those attendees travelling to east London from cities not currently served by its network.
In doing so, it is hoped the collaboration will boost footfall and add “significant” benefit to organisers opting for the Excel as its host venue.
He said: “To have this incredible conference facility outside the airport is amazing and to develop this relationship is fantastic for us.
“The big thing we want to show is versatility and flexibility and just providing customer service to people. We are going to have to work at this partnership.
“We have to understand the people who are putting together conferences so we know exactly who to target."
He added CityJet had just ordered two new aircraft fleet - the CRJ900 and Sukhoi SuperJet 100s - which would have certification to fly from Docklands in 2017.
Meanwhile, aviation fans will spot the co-branding of CityJet-owned aircraft with the Official Airline Partner of Excel emblem.
CityJet will also promote its brand from within the venue.
Mr Pegler said: “This is the first deal [like this] we have ever done because this is the first company we feel shared the same ambitions and principles.
“We want to be the world number one events destination and we want to be the place people aspire to host their events."
London City Airport CEO Declan Collier added: “The partnership will help extend that offer beyond the flight and the airport to the venue, to create a connected, end-to-end journey.”