This paper analyzes the impact of capacity drop on commuters’ travel choice behaviors under uncertainty. For clarity, we assume that the capacity drop is triggered by the queue forming at the bottleneck under the hypercongestion circumstances, and the stochasticity of the drop could not be neglected. Considering the uncertainty of travel time, we establish a bottleneck model with commuters choosing their departure time according to the mean travel cost. From the proposed model, analytical solutions are achieved and therefore several properties are presented, including monotonicity of travel cost and departure rate, and the relationship between dispersion degree and length of peak period. To alleviate traffic congestion at the bottleneck and avoid capacity drop, we design a time-varying toll scheme and a step toll scheme. Evolution of queue length in equilibrium is discussed based on the Laih model. Numerical examples are also presented to demonstrate the established model and the effectiveness of the proposed toll schemes.