Objectives: To elucidate the clinico-laboratory characteristics associated with pediatric systemic lupus erythematosus (pSLE) patients with higher Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) score in a retrospective cohort of pSLE patients. Methods: A retrospective study involving 32 pSLE patients was conducted at Hospital Universiti Sains Malaysia, Kelantan, Malaysia between 2006 and 2017. Results: Within the group of 32 pSLE patients, 23 were girls and 9 were boys (3: 1 ratio). The most common symptom was renal disorder (n = 21; 65.6%) followed by malar rash (n = 9; 28.1%), oral ulcers (n = 7; 21.9%), prolonged fever (n = 5; 15.6%) and arthritis (n = 4; 12.5%). Antinuclear antibodies (ANA) were detected in all patients and 25 patients (78.1%) were positive for anti-double stranded DNA (anti-dsDNA) antibodies. Eighteen (56.3%) patients had active SLE (SLEDAI = 6), and these patients were significantly associated with heavy pyuria (p = 0.004), a high ANA concentration (1: 160; p = 0.040, 1: 320; p = 0.006), elevated ESR (p = 0.006), low C3 levels (p = 0.008), oral ulcers (p = 0.010), heavy hematuria (p = 0.017) and heavy proteinuria (p = 0.017), lupus erythematosus (LE)-nonspecific lesion manifestations (p = 0.019) and malar rash (p = 0.044). Conclusion: Pediatric systemic lupus erythematosus patients with higher SLEDAI score were most significantly associated with pyuria, high ANA titers, and elevated ESR.