The World Health Organization had endorsed Xpert® MTB/RIF (Xpert) as the initial diagnostic for multidrug-resistant tuberculosis (TB) or TB suspects co-infected with the human immunodeficiency virus. We investigated an unexpected case of rifampicin (RMP) resistance on Xpert using repeat Xpert, smear microscopy, MTBDRplus assay, culture, drug susceptibility testing, spoligotyping and rpoB gene sequencing. A false-positive result was most likely, given the wild type rpoB gene sequence and exclusion of both mixed infection and mixture of drug-susceptible and drug-resistant populations. When decentralising Xpert, test performance characteristics need to be understood by health care workers and methods of confirmation of RMP resistance need to be accessible.