Background: The immune system plays a crucial role in cancer surveillance. Lymphopenia during cancer treatment portends poor prognosis. Here, we aim to quantify lymphocyte count changes during radiotherapy (RT) for patients with hepatocellular carcinoma (HCC) treated with proton or photon RT. Methods: Patients with HCC treated with definitive RT from 2006 to 2016 with ≥3 months follow-up were studied. Patient characteristics, tumor features, treatment specifics were recorded. Serial absolute lymphocyte counts (ALC) were collected and graded according to CTCAE v4.0. Overall survival (OS) and distant metastasis free survival (DMFS) were analysed using the Kaplan-Meier method. To investigate difference in ALC between treatment modalities, we performed a paired cohort analysis (15 proton and 15 photon cases, matched to treatment volume). Results: 110 patients were studied. Median age was 67 years. 70% of the cohort had Child-Pugh A5 liver disease and 54% had venous tumor thrombosis (VTT). 75 (68%) had photon RT and 35 (32%) had proton RT. Median OS was 13 months. Overall, there was a 60% drop in ALC during RT. Splenic volume correlated with Grade 3 (G3) lymphopenia (p < 0.0001). Pre-treatment ALC and splenic volume did not correlate with OS or DMFS. Patients who had G3 lymphopenia during RT had poorer DMFS (14 vs 34 months, p = 0.006) and OS (16 vs 34 months, p = 0.015) than their counterparts. Those who received proton RT had a higher ALC nadir (0.56 vs 0.40 k/ul, p = 0.041), lower rate of ALC drop (0.07 vs 0.05 k/ul/day) and better OS (30 vs 22 months) than those who had photon RT. Paired cohort dosimetric analyses revealed that there was a significantly higher low dose volume in the photon group (V1Gy and V10Gy, p < 0.0001 for both; V5Gy, p = 0.002). Higher volume of low dose bath correlated with lower ALC (r = -0.34, p = 0.06 for V1Gy; r = -0.44, p = 0.01 for V5Gy; r = -0.51, p = 0.004 for V10Gy). Splenic irradiation dose correlated with ALC nadir, and proton cases had significantly less splenic dose (p < 0.0001). Conclusions: G3 lymphopenia during RT portends poorer outcomes for patients with HCC. Protons may mitigate RT-induced lymphopenia. An ongoing phase III trial will compare proton and photon RT for HCC to determine the effect on OS.