The role of autophagy in ionizing radiation (IR)-induced primary ciliogenesis in glioblastoma cells was explored. M059K and M059J cells underwent treatment with either 10 Gy of X-rays or serum starvation (SS) for three days. Subsequently, the primary cilia were examined through immunofluorescence staining targeting ciliary markers Arl13b and γ-tubulin. Cellular autophagy levels were estimated by immunofluorescence staining for the autophagy marker LC3 and immunoblotting analysis of p62. To assess primary ciliogenesis, M059K and M059J cells were treated with chloroquine (CQ) or rapamycin (RAPA), which respectively suppressed or activated cellular autophagy. The findings revealed that in M059K, the proportion of ciliated cells was approximately 40%, and this proportion increased to over 75% on day 3 post-irradiation in cells treated with 10 Gy of X-rays (p<0.01). However, the frequency of primary cilia in M059J cells (~7%) showed no obvious changes before and after X-ray irradiation. Interestingly, the proportion of ciliated cells boosted to approximately 80% (p<0.01) and 50% (p<0.01) in M059K and M059J cells starved for 3 d, respectively. Serum starvation (SS) elevated cellular autophagy levels in both cell lines, whereas X-ray irradiation enhanced autophagy levels only in M059K but not in M059J cells. Moreover, activation of autophagy using RAPA facilitated ciliogenesis in both cell lines, while the suppression of autophagy with CQ mitigated IR-induced cilia formation in M059K and SS-induced cilia formation in M059J cells. In summary, these results demonstrate that different cellular autophagy responses to IR in M059K and M059J cells participated in primary ciliogenesis elicited by IR exposure.