The majority of railway incidents result neither in passenger nor operators harm, nor they lead to any severe damage on the rolling stock or the infrastructure. Nevertheless, such incidents result in financial loses, broadly known as indirect costs, which are difficult to identify, isolate, evaluate, and quantify. This paper introduces a framework to quantify the indirect costs in railway operations. Furthermore, as degraded human performance remains a major contributor to operational errors and railway incidents, this study explores for associations between the indirect costs and the factors that affect and contribute to degraded human performance. The framework was implemented in the calculation of the Category A1 Signals Passed at Danger (SPADs) indirect costs. Data was obtained from two UK train operators, while the associated human performance was analysed using the Railway-Performance Shaping Factors (R-PSFs) taxonomy. Employing Spearman's rank order correlation and Fisher's exact statistical tests the associations between R-PSFs and indirect costs were reviewed. Results show significant correlations between the R-PSFs and indirect costs, but only if the importance and severity of every individual R-PSFs is considered. We expect our findings to aid the relevant stakeholders on their efforts to make better decisions on improving safety performance of railway operations.