Kalanchoe pinnata (Lmk) Pers (KP) has an immunosuppressive effect on delayed-type hypersensitivity test. Based on it, this research aimed to determine the repairing effects of aqueous extract of KP on lupus nephritis mice and identified its active compound. The KP extract profile was determined using UPLC-QTOF-MS/MS instrument. We examined six mice groups consisting of three curative treatment groups, one standard group receiving prednisone, one preventive group receiving KP extract, and one healthy (healthy and untreated) group. At the end of the experiment, we measured the proteinuria and renal histology parameters. To recognize the active compound in the KP profile, we performed in silico assays for the flavonoid compounds to bind to the glucocorticoid receptor. We played in silico tests for the flavonoid compounds to identify the active compound in the KP profile. We found the repairing effect of KP was detected in the kidney, demonstrated by its low proteinuria level and its better tissue structure. In the curative group, the urine protein level and its glomerular inflammation decreased. In the preventive group, the aqueous extract of KP could prevent lupus nephritis manifestations in the kidney. Bryophyllin A is the most active compound of the KP. However, further research is needed to understand the mechanism involved. We conclude, the aqueous extract, especially its bryophyllin A, have beneficial effects in repairing the function and tissue structure of lupus manifestations in mice kidney.