Silent aspiration is common after stroke and can lead to subsequent pneumonia. While standard bedside dysphagia assessments are ineffective at predicting silent aspiration, cough reflex testing (CRT) has shown promise for identifying patients at risk of silent aspiration. We investigated the impact of CRT on patient and service outcomes when embedded into a clinical pathway. 488 acute stoke patients were randomly allocated to receive either CRT or standard care (i.e. bedside assessment). Primary outcomes included confirmed pneumonia within 3 months post stroke and length of acute inpatient stay. Secondary outcomes related to the feasibility of implementing a CRT pathway and clinician and patient satisfaction. There was a non-significant reduction in pneumonia rates by 2.2% points in the CRT group (OR 0.32, 95% CI 0.06–1.62). There was a non-significant difference of 0.7 days (95% CI − 0.29 to 1.71 days) in length of stay between the standard care group and the CRT group. The CRT took on average 3 min longer to complete (p < 0.01) and resulted in a significant 6.7% increase in videofluoroscopic referrals (p = 0.02); however, these results are clinically insignificant. High patient and clinician satisfaction with CRT was found, with clinicians reporting additional knowledge and confidence in decision making for dysphagia management. Post hoc subgroup analyses according to stroke types were conducted and revealed no significant differences in pneumonia rates after adjustment for multiple comparisons. In conclusion, it was possible to implement a CRT pathway with minimal increases in clinician resources. While clinicians perceived CRT as beneficial in clinical decision making, the efficacy of CRT for reducing pneumonia rates in acute stroke remains to be established. Clinical Trial Registration-URL: http://www.anzctr.org.au. Unique identifier: ACTRN12616000724471.