You might consider putting a filter inductor in series with your LEDs. That would smooth the current through them and reduce flicker. If V is the voltage your PWM switches between (in volts), I is the current your LED string draws when on (in amps), and t is the time period of the PWM frequency (in seconds), you can start with an inductor of L = 2 * V * t / I henries. Make sure the inductor will handle the LED string current.
For example, if your PWM switches 0 - 24 V, your LEDs draw 20 mA, and your PWM switching cycle is 10 us (100 kHz rate), L = 2 * 24 * 10e-6 / 20e-3 = 24e-3 or 24 mH (millihenries). Larger inductors would smooth the current more.