The folding mechanisms of proteins with multi-state transitions, the role of the intermediate states, and the precise mechanism how each transition occurs are significant on-going research issues. In this study, we investigate ferredoxin-like fold proteins which have a simple topology and multi-state transitions. We analyze the folding processes by means of a coarse-grained Gō model. We are able to reproduce the differences in the folding mechanisms between U1A, which has a high-free-energy intermediate state, and ADA2h and S6, which fold into the native structure through two-state transitions. The folding pathways of U1A, ADA2h, S6, and the S6 circular permutant, S6_p54-55, are reproduced and compared with experimental observations. We show that the ferredoxin-like fold contains two common regions consisting folding cores as predicted in other studies and that U1A produces an intermediate state due to the distinct cooperative folding of each core. However, because one of the cores of S6 loses its cooperativity and the two cores of ADA2h are tightly coupled, these proteins fold into the native structure through a two-state mechanism. Proteins 2014; 82:954–965. © 2013 Wiley Periodicals, Inc.