The Habitable Exoplanet Imaging Mission (HabEx) is a concept for a mission to directly image planetary systems around Sun-like stars and to perform general astrophysics investigations being studied as part of a number of mission concepts for the upcoming 2020 Astrophysics Decadal Survey. HabEx would help assess the prevalence of habitable planets in our galaxy, searching in particular for potential biosignatures in the atmospheres of planets in habitable zones. More generally, HabEx would image our neighboring solar systems and characterize the variety of planets that inhabits them. Its direct imaging capability would also enable the mission to study the structure and evolution of debris disks around nearby stars, and their dynamical interaction with planets. Additionally, it will explore a number of more general astrophysics phenomena in our solar system, galaxy, and beyond, in the UV through NIR range. The exoplanet science goals lead to a mission concept with requirements for high contrast imaging and the continuous spectral coverage. The baseline for HabEx is a 4-meter diameter off-axis telescope designed to both search for habitable planets and perform general astrophysics observations, possibly combined with a starshade. In this paper, the initial flight system design for both the telescope and the starshade are presented, focusing on the key and driving requirements and subsystems, as well as the trajectory and station keeping and formation flying technique. Furthermore, some of the initial design trades undergone are described, as well as the key challenges and enablers. Finally, some of the future design and architecture trades to be performed within the flight systems as part of the continuing effort in the HabEx study are discussed.