To improve the processing efficiency and extend the tuning range of 3D isotropic fabrication, we apply the simultaneous spatiotemporal focusing (SSTF) technique to a high-repetition-rate femtosecond (fs) fiber laser system. In the SSTF scheme, we propose a pulse compensation scheme for the fiber laser with a narrow spectral bandwidth by building an extra-cavity pulse stretcher. We further demonstrate truly 3D isotropic microfabrication in photosensitive glass with a tunable resolution ranging from 8 μm to 22 μm using the SSTF of fs laser pulses. Moreover, we systematically investigate the influences of pulse energy, writing speed, processing depth, and spherical aberration on the fabrication resolution. As a proof-of-concept demonstration, the SSTF scheme was further employed for the fs laser-assisted etching of complicated glass microfluidic structures with 3D uniform sizes. The developed technique can be extended to many applications such as advanced photonics, 3D biomimetic printing, micro-electromechanical systems, and lab-on-a-chips.