The purpose of this study is to improve the qualitative and quantitative image quality of the time-resolved angiography with interleaved stochastic trajectories technique (4D-TWIST-MRA) using deep neural network (DNN)-based MR image reconstruction software. A total of 520 consecutive patients underwent 4D-TWIST-MRA for ischemic stroke or intracranial vessel stenosis evaluation. Four-dimensional DNN-reconstructed MRA (4D-DNR) was generated using commercially available software (SwiftMR v.3.0.0.0, AIRS Medical, Seoul, Republic of Korea). Among those evaluated, 397 (76.3%) patients received concurrent time-of-flight MRA (TOF-MRA) to compare the signal-to-noise ratio (SNR), image quality, noise, sharpness, vascular conspicuity, and degree of venous contamination with a 5-point Likert scale. Two radiologists independently evaluated the detection rate of intracranial aneurysm in TOF-MRA, 4D-TWIST-MRA, and 4D-DNR in separate sessions. The other 123 (23.7%) patients received 4D-TWIST-MRA due to a suspicion of acute ischemic stroke. The confidence level and decision time for large vessel occlusion were evaluated in these patients. In qualitative analysis, 4D-DNR demonstrated better overall image quality, sharpness, vascular conspicuity, and noise reduction compared to 4D-TWIST-MRA. Moreover, 4D-DNR exhibited a higher SNR than 4D-TWIST-MRA. The venous contamination and aneurysm detection rates were not significantly different between the two MRA images. When compared to TOF-MRA, 4D-CE-MRA underestimated the aneurysm size (2.66 ± 0.51 vs. 1.75 ± 0.62, p = 0.029); however, 4D-DNR showed no significant difference in size compared to TOF-MRA (2.66 ± 0.51 vs. 2.10 ± 0.41, p = 0.327). In the diagnosis of large vessel occlusion, 4D-DNR showed a better confidence level and shorter decision time than 4D-TWIST-MRA. DNN reconstruction may improve the qualitative and quantitative image quality of 4D-TWIST-MRA, and also enhance diagnostic performance for intracranial aneurysm and large vessel occlusion.