We demonstrate, for the first time to the best of our knowledge, an all fiber actively Q-switched Yb-doped laser generating cylindrical vector beams (CVBs) based on a fused mode coupler as the transverse mode converter and selector, and an acousto-optic modulator as the active Q-switching element. The radially and azimuthally polarized beams can be switched by adjusting the polarization controllers in the fiber ring cavity, with high mode purities measured to be >93.5%. Stable ns pulses with repetition rate from 30 Hz to 27 kHz were achieved near the wavelength of 1.0 μm. The actively Q-switched CVB with a pulse width of 68 ns, a pulse energy of 3.46 μJ and a peak power of 50.1 W has been obtained when the repetition rate is 30 Hz and the pump power is 150 mW. This flexible Q-switched fiber laser with pulsed CVB output could find potential applications in the fields of materials processing, nonlinear optics and so on.