Abstract Background and Aims IgA nephropathy is the most common primary glomerulonephritis in the Asia–Pacific region, including Japan, and often leads to dialysis initiation. The etiology of IgA nephropathy remains unclear; however, focal infections such as chronic tonsillitis are proposed. Although tonsillectomy should not be performed for Caucasian IgA nephropathy patients, some Japanese studies reported that the combination of steroid pulse therapy with tonsillectomy (TSP) was more effective than steroid pulse therapy alone for the remission of urinary findings. However, the immunosuppressive treatment regimens vary among studies, and treatment effect of combination therapy in preventing renal functional decline is unclear. This study aimed to compare the efficacy of steroid pulse therapy alone versus TSP in improving the remission rate of urinary findings and preventing renal functional decline. Method This retrospective observational study included 116 patients diagnosed with IgA nephropathy based on renal biopsy and treated between January 1, 2010 and December 31, 2020 in Gifu University Hospital. TSP group underwent tonsillectomy received 0.5 g/day of methylprednisolone intravenously for 3 consecutive days at 1-3 weeks. TSP and steroid pulse therapy alone group had 83 and 33 patients, respectively. Of these, 25 patients per group were matched using propensity score matching based on clinicopathologic factors including age, urinary protein level, estimated glomerular filtration rate (eGFR), and the risk classification for progression to end-stage renal disease. The remission rate of urinary findings and the change in eGFR one year after treatment initiation were compared between the two groups. Remission of urinary findings was defined as a urinary protein level of <150 mg/day and <5 erythrocytes/high-power field in the urine sediment. Results The TSP and steroid pulse therapy alone groups did not significantly differ in baseline characteristics including median age (interquartile range) (58 [47–63] and 56 [49–68] years, respectively), female sex (9 and 7, respectively), mean eGFR (60 ± 20 and 63 ± 21 mL/min/1.73 m2, respectively), median urinary protein level (764 [440–1,472] and 990 [425–1,872] mg/day, respectively) (p > 0.05 for all). The remission rate of urinary findings was significantly higher in the TSP group than in the steroid pulse therapy alone group (72% vs. 20%; p < 0.001, χ2 test). Albeit statistically nonsignificant, the decline in eGFR was smaller in the TSP group than that in the steroid pulse therapy alone group (−1.5 ± 8.1 vs −3.7 ± 10.5 mL/min/1.73 m2, p = 0.416; t test). No severe side effect was observed in both treatment groups. Conclusion The higher remission rate of urinary findings observed in the TSP group compared to the steroid pulse alone group suggested that the addition of tonsillectomy to steroid pulse therapy was a clinically effective treatment for IgA nephropathy. Albeit not significant, the TSP group tended to have a smaller decline in eGFR reduction at one-year follow-up, indicating the need for further studies with long-term observation.