To understand the magnetic properties of Fe$_3$GeTe$_2$, we performed the detailed first-principles study. Contrary to the conventional wisdom, it is unambiguously shown that Fe$_3$GeTe$_2$ is not ferromagnetic but antiferromagnetic carrying zero net moment in its stoichiometric phase. Fe defect and hole doping are the keys to make this material ferromagnetic, which are shown by the magnetic force response as well as the total energy calculation with the explicit Fe defects and the varied system charges. Further, we found that the electron doping also induces the antiferro- to ferromagnetic transition. It is a crucial factor to understand the notable recent experiment of gate-controlled ferromagnetism. Our results not only unveil the origin of ferromagnetism of this material but also show how it can be manipulated with defect and doping.