Aim: NICE's highly specialized technology (HST) evaluations are highly restrictive in terms of entry criteria and as a consequence, the vast majority of rare disease medicines are assessed through NICE's standard, single technology appraisal (STA) route. We explored whether NICE shows flexibility and pragmatism when evaluating treatments for rare diseases through its STA process. Materials & methods: We matched a sample of recent, randomly selected STAs for rare diseases to STAs for non-rare diseases and conducted a thematic analysis to identify patterns in NICE's decision-making, with a specific focus on the application of NICE's published methods and the handling of uncertainty. Results: Three themes emerged where some flexibility was shown: 'handling of uncertainty and discretion', 'application of NICE methods' and 'commercial arrangements'. Rare disease technologies were generally subject to longer appraisal times than those for non-rare diseases. Conclusion: Although NICE shows a degree of flexibility and pragmatism toward uncertainties in the evidence base for rare disease medicines, this is often off-set by a lengthy appraisal process, which can lead to delays in patients receiving vital treatment.