This report describes the diagnosis and successful treatment of multiple extrapulmonary sequelae of Rhodococcus equi (R. equi) pneumonia in a 3-month-old filly. Bilateral uveitis and hyphaema, haemolytic anaemia and polysynovitis developed in this foal and were likely due to immune-mediated mechanisms. The challenges associated with diagnosis and treatments of these extrapulmonary disorders are discussed. The filly was treated initially with clarithromycin and rifampin; however, a blood transfusion and immunosuppressive therapy with dexamethasone were required due to progressive haemolysis and for treatment of uveitis and polysynovitis. Bilateral hyphaema was successfully treated with intracameral injections of a recombinant tissue plasminogen activator. The development of antimicrobial resistance in R. equi was an additional challenge encountered in the management of this case and emphasises the importance of culture and in vitro antimicrobial susceptibility testing of isolates from foals with R. equi pneumonia.