In this paper, a new histogram based auto-focusing method for thermal cameras is proposed. This proposed method is realized by FPGA (Field Programmable Gate Array) and DSP (Digital Signal Processor) working together and simultaneously. HF (High Frequency) component, obtained from real-time image flow by FPGA and DSP is used for auto-focusing process. Proposed method is able to determine the focus direction from the HF component produced in the process of histogram equalization by FPGA, unlike Fourier transform and pixel differenve based methods in the literature. With this superiority, proposed method requires no extra calculation for thermal cameras for which histogram equalization is necessary. Analysis show that proposed method is successful on the simulations and scanning thermal cameras.