The offer is available to agents booking through the GDS using UK BSP, and will be deducted automatically at time of bookings.
The Cypriot airline currently operates 20 flights a week from the UK, including a daily Heathrow-Larnaca service.
It also operates Gatwick-Larnaca six days a week, Stansted-Larnaca three times a week, and Gatwick-Athens and Manchester-Larnaca twice a week.
Paul Simmons, Cobalt Air’s chief commercial officer, said: “At Cobalt, we value and understand the role travel agents play in our industry.
"We also understand that it is sometimes a good idea to give our partners in the trade a small advantage over other channels.
“This is why we have launched a 3% commission scheme via BSP on all Cobalt Air bookings between now and December 31, 2018.”