The use of plant extracts with antifungal effects is a plausible alternative solution which is increasingly attracting the attention of researchers worldwide, to address the multiple limitations associated with the use of synthetic agrochemicals. The antifungal potential of essential oils (EO) fractions of Callistemon citrinus, were investigated in vitro by the supplemented media method against Bipolaris oryzae and Alternaria padwickii, two seed-borne fungi of rice in Cameroon. The EO fractions obtained by hydrodistillation of the plant’s fresh and dry leaves inhibited to varying degrees the mycelia growth of the two pathogens. The EO’s fractions obtained from dry leaves were more active than those extracted from fresh leaves. Fractions of EO showed fungicidal effects, with minimum inhibitory concentrations (MIC) varying between 3616 and 7232 μg/ml. The dry leaves EO fraction DF2 exhibited the strongest antifungal activity (MIC = 3616 μg/ml), followed by the fresh leaves fraction FF2 (MIC = 4520 μg/ml) and the total dry leaves EO DM (MIC = 4520 μg/ml), against B. oryzae. Those fractions (DF2, FF2 and DM) also exhibited the highest MIC (MIC = 4520 μg/ml) against Alternaria padwickii. The GC-SM analysis of EO fractions showed that, the antifungal activity was inversely associated to the content of the major bioactive compound 1,8-cineole; 60.67, 66.36 and 86.39% 86.39%; and proportional to α-terpineol; 13.39, 10.52 and 3.5%; for EO fractions DF2, FF2 and MD DM, respectively. Seed treatment of three of rice varieties with fractions DF2, FF2 and DM respectively at the doses of 1.5, 2 and 3.5%, reduced the seed to seedling transmission rate of B. oryzae by 100% and increased the germination rate of these seeds between 2 and 12%. Our results suggest the use of EO from C. citrinus as biofungicides for the treatment of rice seeds infected with B. oryzae and A. padwickii.