Aluminum (Al) is known to inhibit plant growth and limit crop yields in acid areas. This study aimed to investigate the effect of endophytic fungus Glomerella sp. JP4 infection on the growth, photosynthetic pigments, antioxidant enzyme activities, organic acids contents, and Al content of endophyte-infected rice seedlings (EI) and endophyte-uninfected rice seedlings (EF) exposed to Al stress for 9 days. Al stress decreased shoot height, root length, and dry weight of EF plants. Endophyte infection increased the growth parameters except for root length. Compared to EF plants, the chlorophyll a+b content and carotenoid content were significantly enhanced in the EI plants. Antioxidant enzyme activity was also increased in the EI plants compared to the EF plants subjected to Al stress, while malondialdehyde (MDA) content was remarkably reduced. Endophytic infection significantly increased the contents of citrate and succinate in leaves, as well as that of lactate, malate, fumarate, and succinate in roots under Al stress. Endophyte infection decreased the Al content in the shoots and the roots and restricted the Al transfer from the roots to the shoots in the EI plants compared to the EF plants. Our results indicated that infection with endophytic fungus JP4 in the roots had an active role in promoting plant growth, alleviating the phytotoxic effects caused by Al exposure.