Background: Classical Hodgkin lymphoma (cHL) is a rare B-cell malignant neoplasm, characterized by the presence of rare mononucleated Hodgkin and multinucleated Reed–Sternberg cells (HRS). CD34+ cells are highly expressed on lymphoma stem cells in bone marrow (BM). Little is known about gene mutations in BM CD34+ cells of cHL. In this study, whole exome sequencing (WES) was performed and high-frequency mutation genes were examined through their expression levels. Materials and Methods: The influence of the variants on protein function was predicted with in silico tools or public databases. Gene expression levels were determined by quantitative real-time PCR. Results: WES assay from BM CD34+ cells in thirty cHL patients revealed that three variants were detected in known cHL-associated genes, including NCF1 (13.33%), MMP9 (3.33%), and VDR (3.33%). We also observed other candidate genes including CNN2 rs77830704 (76.67%), CNN2 rs78386506 (63.33%), MUC4 p.Y3278_Q3209Del (66.67%), MUC4 p.P1076_P1124Del (33.33%), MUC4 rs748236754 (26.67%), MUC4 p.P1609Ins (23.33%), MUC4 rs748705487 (20%), MUC4 p.P4121_P4137Del (16.67%), MTSS2 rs531163149 (13.33%), KMT2C rs201834857 (20%), HAVCR2 rs184868814 (16.67%), and TCF19 rs541001159 (13.33%). Moreover, the low levels of MUC4 were associated with an increase in neutrophil-to-lymphocyte ratio and the low CNN2 expression group had higher levels of LDH, suggesting that the low expressions of CNN2 and MUC4 might be important risk factors for poor prognosis in cHL. Conclusions: WES revealed significantly mutated genes, most of which were associated with the physiological activation of lymphoma cells. This finding contributed to the identification of novel gene variants that might impact on the function of BM CD34+ cells in cHL patients.