The Operating System scheduler is designed to allocate the CPU resources appropriately to all processes. The Linux Completely Fair Scheduler (CFS) design ensures fairness among tasks using the thread fair scheduling algorithm. This algorithm ensures allocation of resources based on the number of threads in the system and not within executing programs. Fairness issue of the CFS used in Linux kernel comes up due to the fact that programs with higher number of threads are favored by the scheduler, which based on the number of threads in the system. A novel algorithm as well as its implementation through optimized procedure is proposed as a solution to achieving better fairness by punishing greedy-threaded programs. Several tests are conducted to illustrate fairness issue and to examine the effect of the proposed algorithm.