An economic model was developed with guidance from the National Institute for Health and Care Excellence (NICE) 'Managing Common Infections' (MCI) Committee to evaluate the cost effectiveness of different antibiotic treatment sequences for treating Clostridioides difficile infection (CDI) in England. The model consisted of a 90-day decision tree followed by a lifetime cohort Markov model. Efficacy data were taken from a network meta-analysis and published literature, while cost, utility and mortality data were taken from published literature. A treatment sequence was defined as a first-line intervention or a different second-line intervention, and used constant third- and fourth-line interventions. The possible first- and second-line interventions were vancomycin, metronidazole, teicoplanin and fidaxomicin (standard and extended regimens). Total costs and quality-adjusted life-years (QALYs) were calculated and were used to run a fully incremental cost-effectiveness analysis. Threshold analysis was conducted around pricing. Sequences including teicoplanin, fidaxomicin (extended regimen) and second-line metronidazole were excluded based on recommendations from the committee. The final pairwise comparison was between first-line vancomycin and second-line fidaxomicin (VAN-FID), and the reverse (FID-VAN). The incremental cost-effectiveness ratio for FID-VAN compared with VAN-FID was £156,000 per QALY gained, and FID-VAN had a 0.2% likelihood of being cost effective at a £20,000 threshold. First-line vancomycin and second-line fidaxomicin was the most cost-effective treatment sequence at the NICE threshold for treating CDI in England. The main limitation of this study was that the initial cure and recurrence rates of each intervention were applied constantly across each line of treatment and each round of recurrence.