Generating PWM using Arduino Uno and Simulink (interfacing) pins 5 and 6. What's the maximum frequency? I am building a boost converter using a mosfet. The mosfet is driven by PWM generated by an Arduino Uno through Matlab Simulink. In Simulink I am giving 10 KHz pulse width 50%. Practically 10 KHz available at pins 5 and 6. Up to how much frequency can pins 5 and 6 handle?
See my page about timers. The maximum frequency the hardware can output is 8 MHz if you are running a 16 MHz clock.

10 kHz should be easily achievable if you tweak the hardware registers, as Gerben said.