Background: Candidiasis is considered the most significant fungal infection with increasingly reported antifungal resistance, especially against fluconazole. Aim: This study aimed to determine rates of antifungal resistance among Candida isolates from pediatric clinical samples, and test the in-vitro efficacy of natural essential oils against fluconazole-resistant isolates. Methods: Identification and antifungal susceptibility testing were performed utilizing the Vitek2 compact automated system. Fluconazole-resistant Candida isolates were subjected to in-vitro screening for the efficacy of nine natural oils by disc diffusion method, followed by determining the minimal inhibitory concentration for the most effective oils using broth micro dilution. Results: Out of total cultured samples (n=2120), Candida were isolated at a rate of 6.27% (n= 133), mostly from urine and blood samples. Candida albicans was the most prevalent isolated species (54.9%), followed by Candida tropicalis (33.83%). Fluconazole recorded a higher resistance rate (9%) than the rest of antifungals, with a significantly higher incidence among non-C. albicans Candida species (NCAC) than C. albicans (p <0.05). Cinnamon, cumin, thyme, and lemongrass showed the widest mean of inhibition zones, of which cinnamon oil had the lowest MIC values against Candida isolates. Conclusions: Our study concluded higher predominance of C. albicans over NCAC species, and total fluconazole resistance rate of 9%. cinnamon oil was found to be the most effective oil against fluconazole-resistant isolates.