The focus of this article is to propose two different versions of the Heisenberg uncertainty principle related to the fractional Fourier transform (FrFT). The first version is directly derived using the basic connection between the traditional Fourier transform (FT) and the FrFT, and the second is derived by exploiting time differentiation property and Parseval’s formula for the FrFT. In addition, a weighted uncertainty inequality related to this transformation is investigated. As a simple illustration of the use of the obtained results, we design the fractional characteristic function. An inequality describing the relation between the probability density function and its fractional characteristic function is presented.