Background Systemic lupus Erythematous (SLE) is an autoimmune inflammatory disease characterized by antibodies directed against self-antigens, resulting in multi-organ damage. Up to 20% of cases are diagnosed during childhood with 55% of these patients are expected to develop lupus nephritis (LN). Objective At comparing the efficacy of mycophenolate mofetil versus pulse intravenous cyclophosphamide in induction of remission in pediatric patients with lupus nephritis. Subjects and Methods This is a retrospective study that was conducted in Pediatric Allergy and Immunology Unit, Children’s Hospital, Ain-Shams University from the period of December 2007 to January 2017 on 65 pediatric patients with lupus nephritis taking either cyclophosphamide or Mycophenolate Mofetil as an induction therapy. Patients’ data was gathered from their medical records in the Pediatric Allergy and Immunology Unit, Children’s Hospital, Ain-Shams University. Patients enrolled in the study after consideration of inclusion and exclusion criteria. Results Our studied patients were 65 patients divided into 58(89%) female and 7(11%) male with female: male ratio (8: 1) and their age ranged between (5- 18) years. There was no statistically significant difference between different laboratory parmaters used to compare between both groups (C3, 24 hour urinary protein, anti-DNA). However, the rate of change in SLEADI score was higher in patient receiving Cyclophosphamide and Mycophenolate mofetil, but with no significant difference. Conclusions No significant difference between group taking cyclophosphamide and mycophenolate mofetil.