SUMMARYCache affinity has been proved to have great impact on the performance of packet processing applications on multi-core platforms. Flow-based packet scheduling can make the best of data cache affinity with flow associated data and context structures. However, little work on packet scheduling algorithms has been conducted when it comes to instruction cache (I-Cache) affinity in modified pipelining (MPL) architecture for multi-core systems. In this paper, we propose a protocol-aware packet scheduling (PAPS) algorithm aiming at maximizing I-Cache affinity at protocol dependent stages in MPL architecture for multi-protocol processing (MPP) scenario. The characteristics of applications in MPL are analyzed and a mapping model is introduced to illustrate the procedure of MPP. Besides, a stage processing time model for MPL is presented based on the analysis of multi-core cache hierarchy. PAPS is a kind of flowbased packet scheduling algorithm and it schedules flows in consideration of both application-level protocol of flows and load balancing. Experiments demonstrate that PAPS outperforms the Round Robin algorithm and the HRW-based (HRW) algorithm for MPP applications. In particular, PAPS can eliminate all I-Cache misses at protocol dependent stage and reduce the average CPU cycle consumption per packet by more than 10% in comparison with HRW.