A supply voltage droop, temperature variation and aging effects can generate timing failures during operation. Various adaptive clocking methods have been introduced to resolve the problems. They use a tunable clock to avoid the timing failures rather than using wide design guard bands. However, the system performance analysis becomes complicated in a multi-core system with the adaptive clocking method. In this paper, a queueing theory based system level performance model is proposed to estimate an average response time and power by a closed form equation. Furthermore, for multi-core system with the adaptive clocking, an optimal job scheduling method using the inequality of arithmetic and geometric means is proposed. The proposed optimal job scheduling method relieves a system performance degradation arising from the adaptive clocking. The proposed performance model can analyze the system level performance within ∼3% error compared with a JMT system simulation tool. Experimental results also show that the proposed job scheduling method can obtain a significant performance enhancement than the conventional round-robin method.