The study aimed to evaluate the impact of C. schoenanthus essential oil (CSEO) on the immune system, antioxidant balance, and histological changes in the kidney and spleen of female BALB/C mice. The chemical composition of CSEO was analyzed using GC-MS. Twenty-nine compounds were identified, representing 99.04% of the total detected. The main components were Piperitone (47.93%), Elemol (11.91%), 2-Carene (10.69%), β-eudesmol (7.67%), α-eudesmol (5.12%), and γ-eudesmol (4.24%). The mice were divided into three groups: control, 0.5% CSEO, and 1% CSEO. The effects of CSEO on various markers, including malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD), catalase (CAT), urea, creatinine, and cytokines (IL-4, TNF-α, and TGF-β1), were evaluated. Additionally, kidney and spleen histopathological examinations were conducted. The treatment groups showed a significant increase in IL-4, TNF-α, and TGF-β1 levels compared to the control group, except for G1, which showed a non-significant decrease in TGF-β1 levels. Group 2 exhibited a significant increase in MDA levels compared to the control group, while group 1 had a nonsignificant increase. Both treatments showed a significant increase in GSH levels, while SOD and CAT levels showed a non-significant increase in group 2 and a non-significant decrease in group 1. Urea levels showed a non-significant increase, while creatinine levels were significantly decreased in G2 and non-significantly decreased in G1 compared to the control group. The histopathological examinations revealed congested red pulp with activated hematopoiesis and focal fibrosis in spleen sections of both G1 and G2. The study suggests that medicinal herbs such as CSEO need to be used with caution, and their effects should be evaluated carefully, especially in terms of dose-dependent effects. The results indicate that high doses of CSEO may increase the levels of some cytokines and antioxidants and have harmful effects on kidney architecture, congested red pulp, and fibrosis with increased hematopoiesis. Therefore, the random use of medicinal herbs may have harmful effects and needs to be carefully controlled to ensure safe use.