The influence of co-existing atopy on the prognosis of juvenile systemic lupus erythematosus (JSLE) was assessed in this study. Patients diagnosed with JSLE between October 2005 and April 2016 were enrolled in a prospective study and followed up for 2 years. Management of patients was evaluated using the systemic lupus erythematosus disease activity index 2000 (SLEDAI-2K) score and laboratory variables. Eighty JSLE patients were enrolled at diagnosis and divided into those with (n = 35) and without (n = 45) atopy. When compared with the non-atopic group, atopic patients showed higher SLEDAI-2K score at disease onset (16.09 vs. 11.18), higher erythrocyte sedimentation rate (52.89 vs. 38.27 mm/h), higher percentage of total B-cells (25.85 vs. 19.51%), lower percentage (7.26 vs. 9.03%) and cytotoxicity (9.92 vs. 11.32%) of natural killer cells, and lower complement C3 (0.51 vs. 0.69 g/L) (all p<0.05). At 1, 3, 6, 12, 18, and 24 months, JSLE patients with atopy reached higher SLEDAI-2K score and lower ΔSLEDAI-2K improvement rate (at 1 month, 8.34 vs. 4.71 and 43.63 vs. 57.95%, respectively; at 3 months, 8.57 vs. 2.62 and 48.39 vs. 75.10%, respectively; at 6 months, 6.91 vs. 2.38 and 53.59 vs. 77.26%, respectively; at 12 months, 4.71 vs. 1.80 and 69.54 vs. 84.10%, respectively; at 18 months, 4.66 vs. 2.02 and 68.14 vs. 82.93%, respectively; at 24 months, 8.57 vs. 2.62 and 70.00 vs. 81.88%, respectively; all p<0.05). During the 24 months of follow-up, the total number of disease flares was higher in JSLE patients with co-existing atopy (3.77 vs. 1.51, p<0.05), and the atopic group needed much more time to reach the stable condition of the disease (6.88 vs. 4.65 months, p<0.05). JSLE patients combined with co-existing atopy had more severe disease at diagnosis and poorer outcomes than JSLE patients without atopy.