SLE in paediatric patients requires long-term treatment with several side effects. Nigella sativa is known to have immunomodulatory effects. Our study aimed to investigate the immune-modulatory effects of Nigella sativa oil on T lymphocyte activity, inflammatory cytokine profile, and improvement of SLEDAI score in our patients. This was a placebo-controlled clinical trial of Nigella sativa oil administration in 32 paediatric SLE patients who were tested before and after treatment. The study subjects were randomly assigned. Patients had blood samples taken to be tested for T cell ratio, percentage of a number of cytokines (IFN-γ, TNF-α, IL-2, IL-4, IL-6, IL-17, and IL-10) using flow cytometry and CBA (Cytometric Bead Array), and SLEDAI score at the beginning of the study and after treatment. They were treated with 1 gram of N. sativa oil capsules and 1 gram of placebo daily for 8 weeks.