The aim of this study was to determine the prevalence of seed-borne fungal pathogens of jute and their control with plant extract. The experiment was carried out in seed pathology centre, Bangladesh Agricultural University to obtain relevant information about the health of jute seeds and find out the efficacy of extracts as seed-treater. Two varieties viz., Deshipat (Corchorus capsularis) and Tossapat (Corchorus olitorius) were selected for this study and jute seeds were collected from two different locations of Bangladesh. The major predominant identified fungi were Colletotrichum corchori, Macrophomina phaseolina, Fusarium spp., and Botryodiplodia theobromae. Least seed-borne fungi were found in the variety of Tossapat. Low germination of seeds was found related to high prevalence of seed-borne fungal infections. Highest seed-borne infection was obtained in the variety of Deshipat. In this study, we evaluated some major plant extracts such as garlic clove (Allium sativum), neem leaves (Azadirachta indica), allamanda leaves (Allamanda cathartica L.) and marigold leaves (Tagetes spp.) for observing the action of these plant extracts on seed borne fungi of Jute. The study revealed that the extract of Garlic (Allium sativum), and Biskatali (Polygonum hydropiper) increased the germination of seeds and garlic (Allium sativum) extract was also found to be most effective in controlling the seed-borne infection among all the treatments. Although the inhibiting capacity of the extracts of Allamanda (Allamanda cathartica L.) and Biskatali (Polygonum hydropiper) was found to be similar and Biskatali extract was found to have the second position among all the treated plant extracts in inhibiting the growth of isolated fungal pathogens.