Strobilurins, also known as quinone outside inhibitors (QoIs), are one of the most important fungicide groups for controlling plant diseases. In addition, they can prime plants for enhanced defense against pathogen attack. Here, detailed biochemical and microscopic analyses were performed to investigate whether azoxystrobin (Az) could enhance defense responses to Bipolaris oryzae, the cause of brown spot of rice. Fungal infection increased the activity of all defense enzymes regardless of fungicide treatment. Az-sprayed plants displayed higher activities of β-1,3-glucanase, peroxidase, polyphenol oxidase (PPO) and lipoxygenase (LOX) in the absence of B. oryzae inoculation and of phenylalanine ammonia-lyase, PPO and LOX at 24 h after inoculation (hai) with B. oryzae compared to the control plants. Concentrations of total soluble phenols at 144 hai were higher in the Az-sprayed plants relative to their non-treated counterparts. Concentrations of lignin-thioglycolic acid derivatives were increased following fungal infection in the control plants. Hyphae from B. oryzae colonized bulliform, bundle sheath, epidermal, guard, mesophyll and vascular bundle cells besides intercellular spaces, but fewer and smaller fungal cells were noticed in the Azsprayed than in the control plants. Therefore, although Az transiently reprogrammed activities of some defense enzymes, its fungicidal activity appears to have played a major role in reducing B. oryzae infection.