In an actively Q-switched fiber laser (AQS-FL) a type of acousto-optic modulator (AOM) or (potentially) electro-optic modulator (EOM) controls the generation of output nanosecond wide pulses. An integrated Gaussian pulse shape is desirable in many applications such as material processing, microfabrication, ultrasound generation, gold photothermal therapy, etc. However, because of the system dynamics, generation of perfect Gaussian pulse shapes is not guaranteed in an AQS-FL, additionally designing the AQS-FL for a desired pulse peak and duration is an inverse problem which needs cumbersome trialerror efforts. We have developed a framework consisting of a rigorous FDM method plus a dedicated and innovative multi-objective genetic algorithm (GA) which assists the designer in achieving the desired Gaussian pulses within a reasonable time frame. The developed GA evolves the timing parameters of modulator plus the pump power and fiber length until the suitable goal is reached. To demonstrate the flexibility and design feasibility of our GA, three different single pulse and pulse train generation scenarios on a 7.5 m long Ytterbium-doped double clad fiber (YD-DCF) are examined to achieve the Gaussian,150 Wand 200 W peak power, 250 ns and 300 ns width pulses. To the best of our knowledge, it is the first implementation of an intelligent algorithm for optimizing the output pulse of an AQS-FL. It is worth noting that depending on the fiber host material and modulator specifications, much higher peak powers and different pulse durations are feasible, furthermore in case of utilizing the AOM, the pertaining limitations and feasibility are considered.