The pledge comes as part of a new partnership with Durrell Wildlife Conservation Trust.
From Monday (22 November) all Blue Islands seats booked to fly from 1 December will include a £1 carbon offset contribution.
The carrier is also seeking to reduce its environmental impact through a series of "next-generation technologies" and aiming for a longer-term zero-carbon target.
Durrell’s Rewild Carbon programme aims to “revive eco-systems, recover species, reduce carbon and rebuild livelihoods”, with 95% of all funds received going towards its nature projects.
Its first reforestation project is in Brazil’s Atlantic rainforest and aims to create a sustainable eco-system in a "previously ravaged" area.
Rob Veron, Blue Islands chief executive, said: "Connecting people, whether for our social wellbeing or economic prosperity, is an essential part of island life. We recognise that this necessity comes at a cost to our planet, for which we all need to take responsibility, and part of this is ensuring our air services are as sustainable as possible.
"By becoming carbon neutral, we are taking this vital first step in our journey towards our long-term goal of fully replacing the technology that we use. With our heart in the Channel Islands, we’re proud to partner with an organisation that has developed an accountable, transparent and scientific programme to fully balance our carbon impacts for every flight, and that is synonymous with Jersey."