Cassia fistula seeds have many therapeutic uses in traditional medicine practice. The present investigation was undertaken to demonstrate the anticandidal activity of the C. fistula seed extract at ultra-structural level through transmission electron microscope (TEM) and scanning electron microscope (SEM) observations. The effect of seed extract on the growth profile of the Candida albicans was examined via time-kill assays and in vivo efficacy of the extract was tested in an animal model. In addition, the anticandidal effect of seed extract was further evaluated by microscopic observations using SEM and TEM to determine any major alterations in the ultrastructure of C. albicans. The complete inhibition of C. albicans growth was shown by C. fistula seed extract at 6.25 mg/mL concentration. The time-kill assay suggested that C. fistula seed extract had completely inhibited the growth of C. albicans and also exhibited prolonged anti-yeast activity. The SEM and TEM observations carried out to distinguish the metamorphosis in the morphology of control and C. fistula seed extract-treated C. albicans cells revealed the notable effect on the outer cell wall and cytoplasmic content of the C. albicans and complete collapse of yeast cell exposed to seed extract at concentration 6.25 mg/mL at 36 h. The in vitro time-kill study performed using the leaf extract at 1/2, 1 or 2 times of the MIC significantly inhibited the yeast growth with a noticeable drop in optical density (OD) of yeast culture, thus confirming the fungicidal effect of the extract on C. albicans. In addition, in vivo antifungal activity studies on candidiasis in mice showed a 6-fold decrease in C. albicans in kidneys and blood samples in the groups of animals treated with the extract (2.5 g/kg body weight). The results suggested that the C. fistula seed extract possessed good anticandidal activity and is a potential candidate for the development of anticandidal agents.