There is a strong need for an optimized management of the thermal problem in Yb:YAG laser rod and for a powerful, fast, and accurate modeling tool capable of treating the heat source distribution very close to what it actually is. In this paper, a new optimization algorithm called Bacterial Foraging Optimization Algorithm (BFOA) is proposed for simulation of the radial heat distribution. A BFOA discloses a simulation method which delivers the exact temperature distribution in a circularly cylindrical structure with a circularly symmetrical, longitudinally, and transversally non-uniform heat source distribution and circularly symmetrical cooling means. its rod was end pumped with 940 nm and it has been tested with pump power ranging from 1Kw to 2Kw for radius pumping ratio of 1/2, 1/3, and 1/4, for both Top hat and Gaussian beam pumping . The output power is obtained and compared with previously published experimental measurements for different pump power and a good agreement has been found.