Objective To investigate the relationships between circulating tumor cells (CTCs), circulating tumor endothelial cells (CTECs) and treatment methods in patients with nasopharyngeal carcinoma (NPC) at different stages of treatment. Methods The data of NPC patients at different treatment periods in West China Hospital of Sichuan University from March 2016 to November 2019 were retrospectively collected. The patients received CTCs test and part of those patients received CTECs test, by subtraction enrichment-immunostaining-fluorescence in situ hybridization. The relationships of CTCs and CTECs with radiotherapy and chemotherapy, and the correlations between CTCs and CTECs in NPC patients were analyzed. Results A total of 191 patients were included. Among them, there were 66 cases before initial treatment, 38 cases after induction chemotherapy, and 87 cases after concurrent chemoradiotherapy. A total of 127 patients received CTECs test, including 41 cases before initial treatment, 29 cases after induction chemotherapy, and 57 cases after concurrent chemoradiotherapy. The positive rates of CTCs were 89.4%, 81.6% and 69.0% respectively in the three stages of treatment, and the difference was statistically significant only between the pre-treatment group and the post-concurrent chemoradiotherapy group (P=0.003). The number of CTCs in the post-concurrent chemoradiotherapy group was lower than that in the pre-treatment group and the post-induction chemotherapy group (P<0.001, P=0.002). The number of triploid CTCs in the post-concurrent chemoradiotherapy group was significantly different from that in the pre-treatment group and the post-induction chemotherapy group (P=0.009, P=0.013). The number of tetraploid CTCs in the post-concurrent chemoradiotherapy group was significantly different from that in the post-induction chemotherapy group (P=0.007). The number of polyploidy (pentaploid or > 5 copies of chromosome 8) CTCs in the post-concurrent chemoradiotherapy group was significantly different from that in the pre-treatment group (P<0.001). The positive rates of CTECs were 70.7%, 82.8% and 64.9% respectively in the three stages of treatment, and the difference was not statistically significant (P>0.05). The number of CTECs in the post-concurrent chemoradiotherapy group was only lower than that in the post-induction chemotherapy group (P=0.009). There was no significant difference in the number of triploid or tetraploid CTECs among the three groups (P=0.265, P=0.088). The number of polyploid CTECs was statistically different only between the post-concurrent chemoradiotherapy group and the post-induction chemotherapy group (P=0.007). Spearman correlation analysis showed that there was a significant positive correlation between CTCs and CTECs (rs=0.437, P<0.001). Conclusions Concurrent chemoradiotherapy plays a decisive role in reducing the number of CTCs in the blood of NPC patients, while induction chemotherapy does not appear to directly cause changes in the number of CTCs. In NPC patients, different types of CTCs have different responses to different treatments. There is a significant positive correlation between CTECs level and CTCs level in NPC.