Background: Cerebral ischemia-reperfusion injury may simultaneously result in functional variation of multiple genes/pathways. However, most prior time-sequence studies on its pathomechanism only focused on a single gene or pathway. Our study aimed to systematically analyze the time-dependent variation in the expression of multiple pathways and networks within 24 h after cerebral ischemia-reperfusion injury. Results: By uploading 374 ischemia-related genes into the MetaCore software, the variation in the expression of multiple pathways and networks in 3 h, 12 h, and 24 h after cerebral ischemia-reperfusion injury had been analyzed. The conserved TNFR1-signaling pathway, among the top 10 pathways, was consistently enriched in 3h, 12h, and 24h groups. Three overlapping pathways were found between 3h and 12h groups; 2 between 12h and 24h groups; and 1 between 3h and 24h groups. Five, 4, and 6 non-overlapping pathways were observed in 3h, 12h, and 24h groups, respectively. Apart from pathways reported by earlier studies, we identified a novel pathway related to the time-dependent development of cerebral ischemia pathogenesis. The process of apoptosis stimulation by external signals, among the top 10 processes, was consistently enriched in 3h, 12h, and 24h groups; 2, 1, and 2 processes overlapped between 3h and 12h groups, 12h and 24h groups, and 3h and 24h groups, respectively. Four, 5, and 5 non-overlapping processes were found in 3h, 12h and 24h groups, respectively. The presence of apoptotic processes was observed in all the 3 groups; while anti-apoptotic processes only existed in 3h and 12h groups. Additionally, according to node degree, network comparison identified 1, 8, and 5 important genes or proteins (e.g. Pyk2, PKC, E2F1, and VEGF-A) in 3h, 12h, and 24h groups, respectively. The Jaccard similarity index revealed a higher level of similarity between 12h and 24h groups than that between 3h and 12h groups. Conclusion: Time-dependent treatment can be utilized to reduce apoptosis, which may activate anti-apoptotic pathways within 12 h after cerebral ischemia-reperfusion injury. Pathway and network analyses may help identify novel pathways and genes implicated in disease pathogenesis.