Cost overrun is a global issue plaguing transportation infrastructure projects, and the rail industry in the United Kingdom is not exempted. This industry plays a significant role in stimulating the country’s economic development and growth in the United Kingdom (UK). Understanding the factors contributing to cost overruns in rail projects is viable to sustain its contribution, especially in the COVID-19 epidemic era. This study analyzed and predicted the impact of cost overruns on rail projects in the UK in a COVID-19 pandemic era through a sparse network and system dynamics approach. It leverages a review of existing literature and perceptions of 80 construction professionals purposively to establish the factors affecting cost overruns affecting the UK rail construction sector. Findings reveal a web of causations that highlights labor productivity, delay in the supply of construction materials and equipment, and access to the site as fundamental predictors of cost overruns during a COVID-19 pandemic era. The resulting findings are beneficial to assist project managers with the needed awareness to strategically plan and mitigate the potential rise in cost overruns of rail projects in the UK during the pandemic.