Pasteurella multocida is an important veterinary pathogen causing infections in animals and birds. Nowadays, different reports have described the severity of infections, increasing resistance of micro-organisms to antibiotics, and the contribution of ethnoveterinary practices towards the treatment of various ailments of animals. The aim of the present study was to investigate the antibacterial efficacy of the ethanolic extracts of endophytic fungi against P. multocida Capsular Type A strains. A total of six endophytic fungi were isolated from two tropical ethnoveterinary plants: Garcinia xanthochymus H. and Polygonum chinense L. The ethanolic extracts of the endophytic fungi were subjected to in vitro antimicrobial activity by the well diffusion method. Besides, we evaluated the treatment of mice with the potent fungal extract and observed the effects in different organs under electron microscopy. Our results showed that four fungi had antimicrobial activity against the selected pathogen. The best antibacterial activity was showed by the extract of the endophytic fungi, Glomerella magna isolated from G. xanthochymus, with a minimum inhibitory concentration of 46.9 μg/mL and minimum bactericidal concentration of 750 μg/mL. Treatment of mice with the potent fungal extract caused a considerable inhibitory effect on the pathogen growth in vital organs, results that was also confirmed by histopathological studies made by scanning electron microscopy. The present findings indicated that the endophytic fungi G. magna has the potential to provide an effective treatment against infections caused by Pasteurella multocida. However, the isolation of bioactive components needs further investigation.