In this article, we present a new methodology to model patient transitions and length of stay in the emergency department using a series of conditional Coxian phase‐type distributions, with covariates. We reformulate the Coxian models (standard Coxian, Coxian with multiple absorbing states, joint Coxian, and conditional Coxian) to take into account heterogeneity in patient characteristics such as arrival mode, time of admission, and age. The approach differs from previous research in that it reduces the computational time, and it allows the inclusion of patient covariate information directly into the model. The model is applied to emergency department data from University Hospital Limerick in Ireland, where we find broad agreement with a number of commonly used survival models (parametric Weibull and log‐normal regression models and the semiparametric Cox proportional hazards model).