Background: stroke patients often have a combination of sleep apnea syndrome, which is an important and modifiable risk factor for stroke prognosis. Acupuncture is one of the measures for sleep apnea syndrome, and it is also widely used in stroke. However, we are concerned that its efficacy and safety in the treatment of stroke with sleep apnea syndrome are not yet clear. Methods: This systematic review and meta-analysis was performed in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses schema and was registered with INPLASY (registration number: INPLASY202250113). The following 8 databases were searched: PubMed, Cochrane Library (CENTRAL), Embase, Web of Science, China National Knowledge Infrastructure, Chongqing VIP Information, WanFang Data, and China Biomedical Literature Database limited from the establishment of each database to May 4, 2022. Subject headings, free words, and keywords were used for retrieval. Relevant literature was supplemented by consulting other resources. We assessed the risk of bias in the included studies using the Cochrane risk of bias tool. RevMan 5.4 software (The Cochrane Collaboration, 2020) was used to perform the meta-analysis. Results: Six records were included, including a total of 513 participants: 256 in the experimental group and 257 in the control group. The results showed that the total effective rate (relative risk = 1.23, 95% confidence interval (CI): 1.13, 1.34, P < .00001), apnea-hypopnea index (mean difference (MD) = −8.39, 95% CI: −9.19, −7.59, P < .00001), Epworth Sleepiness Scale score (MD = −1.59, 95% CI: −2.66, −0.52, P = .004), minimal oxygen saturation (MD = 4.99, 95% CI: 3.5, 6.47, P < .00001), longest duration of apnea (MD = −7.47, 95% CI: −8.97, −5.97, P < .00001), longest duration of apnea (MD = −6.48, 95% CI: −8.60, −4.35, P < .00001), and S100β levels (standard mean difference = −1.52, 95% CI: −1.87, −1.18, P < .00001) were better in the experimental group than in the control group. Simultaneously, the effect of reducing the neuron-specific enolase level in the experimental group was comparable to that in the control group (MD = -3.40, 95% CI: −9.08, 2.29, P = .24). Conclusions: Acupuncture can improve the clinical symptoms and related laboratory indicators for sleep apnea syndrome in patients with stroke. More high-quality trials remain urgently needed.