The positional isomerization of alkenes is a well-known process mediated by various transition metal complexes. Nevertheless, systems which isomerize alkenes with complete regio- and stereoselectivity are rare. Most reported cases proceed through 1,3-hydrogen shift (allyl) mechanisms, rather than the generally more common 1,2-hydride shift (alkyl) mechanism, provoking consideration of the unique opportunities the former mechanism offers. Accordingly, the first part of this Perspective article will cover stereoselective alkene isomerization systems operating through 1,3-hydrogen shift mechanisms, with an emphasis on the origin of stereocontrol. Next, examples where these systems are employed in tandem with subsequent transformations to rapidly form complex molecular architecture will be discussed, illustrating the potential of alkene isomerization as a strategic tool in stereoselective synthesis.