New generation airborne embedded system has deployed Graphical Processing Units (GPUs) to raise processing capability to meet growing computational demands. Comparing with the cloud system, the airborne embedded system usually has a fixed application set, but strict real-time constraints. Unfortunately, the inherent GPU scheduler does not consider the application priority, which cannot provide the sufficient real-time capability to the airborne embedded system. To meet timeliness requirements, it is necessary to predict timing behaviors of those applications and design a real-time scheduling policy based on priority and deadline. We therefore propose WAMP2S, a workload-aware GPU performance model based pseudo-preemptive real-time scheduling algorithm for the airborne embedded system. The workload-aware GPU performance model can accurately predict the execution time of an application, which is running concurrently with other applications on GPU. The pseudo-preemptive real-time scheduling algorithm can provide the approximate preemption by dynamically adjusting GPU computing resources for active applications. Unlike previous work on GPU performance model and GPU real-time scheduling, WAMP2S considers the impact of co-executing workload on the execution time estimation and provides a software-only approach for preemption support. In addition, WAMP2S implements a prototype GPU scheduler without any source code analysis. We evaluate the proposed GPU performance model and real-time scheduling algorithm in both simulated and realistic application sets. Experimental results illustrate that WAMP2S can achieve low prediction error and high scheduling success ratio.