While the container crane is an important part of daily port operations, it has received little attention in comparison with other infrastructures such as buildings and bridges. Crane collapses owing to earthquakes affect the operation of the port and indirectly impact the economy. This study proposes fragility analyses for various damage levels of a container crane, thus enabling the port owner and partners to better understand the seismic vulnerability presented by container cranes. A large number of nonlinear time-history analyses were applied for a three-dimensional (3D) finite element model to quantify the vulnerability of a Korean case-study container crane considering the uplift and derailment behavior. The uncertainty of the demand and capacity of the crane structures were also considered through random variables, i.e., the elastic modulus of members, ground motion profile, and intensity. The results analyzed in the case of the Korean container crane indicated the probability of exceeding the first uplift with or without derailment before the crane reached the structure’s limit states. This implies that under low seismic excitation, the crane may be derailed without any structural damage. However, when the crane reaches the minor damage state, this condition is always coupled with a certain probability of uplift with or without derailment. Furthermore, this study proposes fragility curves developed for different structural periods to enable port stakeholders to assess the risk of their container crane.