The formation of gums and surface deposits in aircraft fuel systems is known to be caused by oxidative reactions, which occur at elevated temperatures as jet fuel is used as a coolant, or by passive heating during passage through hot engine sections. In this work, we explore the effect of fuel deoxygenation levels on oxidation processes and autoxidative surface deposit formation via experimental and modeling approaches. Experimental measurements of oxygen consumption and deposition are performed over a range of initial oxygen levels in the near-isothermal flowing test rig (NIFTR) heated tube rig and quartz crystal microbalance (QCM) batch reactor systems. In addition, computational fluid dynamic (CFD) simulations, which include an autoxidative chemical kinetic mechanism, are used to help understand the effect of deoxygenation at partial and complete oxygen consumption conditions. The results indicate that under partial oxygen consumption conditions (i.e., high flow rates and relatively low temperatures) deoxygenation may have a significantly reduced effectiveness in eliminating deposit formation unless very high levels of deoxygenation are attained. Conversely, during complete (or nearly complete) oxygen consumption conditions (i.e., low flows and high temperatures) deoxygenation can be very effective. The results show that to be effective under all oxygen consumption conditions, one needs to deoxygenate to a lower level than the amount of oxygen consumed (e.g., 10% oxygen consumption requires deoxygenation to less than 10% of the initial oxygen level). The effect of deoxygenation is a complex function of conditions, such as temperature, flow, and oxygen consumption level, and this work points to the need for careful consideration of these conditions when employing fuel deoxygenation.