Alpha-fetoprotein (AFP) and protein induced by vikamin K antagonist II (PIVKA-II) are useful serum biomarkers to monitor progression of hepatocellular carcinoma (HCC) after proton therapy (PT). Despite the clinical response, however, a transient increase in the biomarkers, so called surge or flare, is frequently observed, which could lead to misinterpretation of tumor progression. In addition, pseudoprogression on diagnostic imaging is also experienced during follow-up. To date, however, few investigators have reported these phenomena after PT, and their mechanisms remain hardly understood. In this study, we investigated changes of AFP and PIVKA-II and pseudoprogression on magnetic resonance imaging (MRI) after PT, and the relationship between this flare phenomenon and clinical response. This study included 60 patients with stage I/II HCC undergoing PT in our institution between September 2013 and March 2016. Patients who were taking warfarin or had a recurrence outside the PT field within 12 months after PT were excluded from analysis. Median serum levels of AFP and PIVKA-II before PT were 13.5 ng/ml (range 1-8,667) and 36 mAU/ml (range 12-35,600), respectively. The delivered dose was 66 GyE in 10 fractions. Serum levels of AFP and PIVKA-II were measured at 1, 3, 6, 9, and 12 months after PT. AFP and PIVKA-II flares were defined as >20% increase in serum levels above 20 ng/ml (AFP) or 40 mAU/ml (PIVKA-II). The size of PT-targeted lesions was measured by MRI. Overall response at 12 months after PT was CR in 55%, PR in 25%, and other in 20%. Among the 60 patients, 4 had a transient rise of AFP, while 23 had a PIVKA-II flare. The median increase rate compared to the level at preceding examinations was 36.5% (range, 30-447%) for AFP and 115% (range, 25-3,740%) for PIVKA-II. The median time to AFP and PIVKA-II flare peaks was 3.5 and 6 months, respectively. AFP and PIVKA-II flares were observed in two consecutive follow-ups in one and 8 patients, respectively. PIVKA-II flares were also observed in inconsecutive follow-ups in 4 patients. Both AFP and PIVKA-II flares were observed in 2 patients. Of them, one patient had simultaneous AFP and PIVKA-II flares at 1 month after PT. Both PIVKA-II flare and pseudoprogression on MRI were observed in 2 patients. Among them, one patient had simultaneous PIVKA-II flare and pseudoprogression at 1 month after PT. No patient had AFP and PIVKA-II flares and pseudoprogression on MRI. Univariate logistic regression analysis showed no relationship between clinical outcome and flares of AFP and PIVKA-II. Increases in AFP and PIVKA-II levels during follow-up after PT should be assessed with caution to avoid misinterpretation of therapeutic outcome. Combination of serum biomarkers of AFP and PIVKA-II and imaging examination is essential to monitor tumor progression after PT.