This study investigated the ability of an endophytic fungus Acremonium alternatum to reduce clubroot formation in the model plant Arabidopsis thaliana, which is highly susceptible to Plasmodiophora brassicae. Quantitative PCR demonstrated that A. alternatum colonized the P. brassicae-infected roots and shoots of the host plant. When Arabidopsis plants were co-inoculated with P. brassicae and A. alternatum, gall formation was reduced as shown by the reduction of the disease index (DI) by up to 50% compared to plants only infected with P. brassicae, whereas the infection rate was lowered by about 20% only in several, but not all, experiments. Clubroot was similarly suppressed when plants were inoculated with autoclaved A. alternatum spores or spore extracts, showing that viable spores were not needed. However, A. alternatum spores did not inhibit P. brassicae resting spore germination. Compared to the normal root galls, the smaller root galls on A. alternatum-inoculated plants contained fewer resting spores of the clubroot pathogen. It was thus hypothesized that inoculation with A. alternatum delayed the development of P. brassicae. Using quantitative RT-PCR to monitor the expression of P. brassicae genes differentially expressed during the development of the disease, a delayed pathogen development was corroborated. Furthermore, greenhouse experiments identified a time window in which the endophyte had to be administered, where the latest effective time point was 5 days before inoculation with P. brassicae and the optimum treatment was to administer A. alternatum and P. brassicae at the same time. These results indicate that A. alternatum and perhaps similar endophytes could be useful for the management of clubroot disease.