We use measured transatlantic flight times since 1994 from the IAGOS (In-Service Aircraft for a Global
Observing System) program to assess the impact of the North Atlantic Oscillation, El Nino-Southern Oscillation, Quasi-Biennial Oscillation and solar cycle. We show that they drive changes to one-way flight times of over an hour and to round-trip flight times by several minutes per flight. They thus cause variability in total CO₂ emissions of 10s of kT/month and financial cost of millions of US dollars/month over the full transatlantic fleet.