Computational combustion modeling is an essential complementary tool to engine experiments and the combination of computational fluid dynamics and detailed chemical kinetics provides the promise for optimizing engine performance. However, predicting the effects of chemical and physical properties of fuels on engine performance is a great challenge since transportation fuels are composed of several hundreds to thousands of chemical species. Surrogates are simpler representations of real fuels and are comprised of selected species of known concentrations that exhibit combustion characteristics similar to those of the real fuels. In this paper, drawing from our previous work on surrogate formulations, we investigate the effects of surrogate components on the autoignition characteristics of conventional and alternative jet fuels, using a combination of experimental and modeling approaches. As target fuels, we analyzed a conventional jet fuel (Jet-A) and two alternative jet fuels (coal-derived IPK, natural-gas-derived S8). Experimental data on the properties of surrogate mixtures, such as liquid density and threshold sooting index, their combustion behaviors, together with those from their corresponding target real fuels are compared and analyzed using predictions obtained from the surrogate model. Results from a modified CFR engine show that the ignition reactivity of Jet-A and Sasol IPK surrogates are stronger than their target fuels, while the S8 surrogate displayed an ignition behavior very similar to the target S8. Results from a constant volume spray combustion chamber provided reasonable agreements between the surrogates and their target jet fuels in terms of physical and chemical ignition delay times and apparent heat release trends, with the S8 surrogate showing the best agreement. In addition, surrogate mixtures that were modified from the original Jet-A and IPK surrogates to achieve a better agreement with CFR experiments performed poorly when tested in a spray chamber. These results imply that the agreement between the behaviors of surrogates and real fuels in one device or in one condition does not guarantee similarity in other devices or in other conditions. This study also highlights the need for improvements in the current surrogate formulation methodologies to provide a more universal emulation of the autoignition behaviors of target transportation fuels.