Purpose: We report the use of a rapid multiplex polymerase chain reaction (PCR) system in the microbiological diagnosis and the therapeutic management of a severe bacterial keratitis case. Observations: During the management of a severe bacterial keratitis case, standard microbiological diagnostic methods were performed. At the same time, an additional ocular swab sampling from the cornea was performed and analyzed using two rapid multiplex PCR assays allowing the simultaneous detection of 29 different virus, yeast and bacteria genomes. Using combination of two rapid multiplex PCR systems, the microbiological diagnosis of a severe Pseudomonas aeruginosa induced keratitis was performed within 90 minutes after an ocular sampling. A rapid subsequent adaptation of local antibiotic treatment was performed allowing to the young patient to regain 6 months after her hospital admission a final visual acuity of 20/20 in her right eye. Conclusions and importance: The present case report suggests that the use of a rapid multiplex PCR strategy may result in a decrease of the mean hospital stage duration for severe infectious keratitis and in an improvement of the clinical outcome of severe keratitis infections. Nevertheless, additional prospective studies are needed to evaluate whether this innovative strategy may replace the current standard approach and optimize the therapeutic management of severe corneal infections.