The display, replicating the same feat from nearly 50 years ago, coincides with the global celebration of 50 years since Mustang debuted at the 1964 World's Fair in New York.
"New York is one of the greatest cities in the world, and it's the place where the Ford Mustang story began 50 years ago," said Mark Fields, Ford Chief Operating Officer.
"We're thrilled to be visiting the architectural landmark that has been the heart of the Manhattan skyline for 83 years with the newest-generation of the car that is the soul of Ford Motor Company."
Taking a car 86 storeys above the densely populated streets of Midtown Manhattan is no simple task.
No portable crane can reach the 86th floor observatory, and the spire towering above the relatively narrow deck makes helicopter delivery impossible. That leaves the lifts as the only viable option.
When the Empire State Building opened in 1931 as the world's then-tallest building - a title it held for nearly 40 years - no one would have envisioned trying to transport a car up in the original lifts.
But in 1965, a prototype Mustang convertible was sliced into three main sections plus windshield so that the sections would fit into those lifts.
"Like all good craftsmen, our team is measuring twice and cutting once to make sure we can get this Mustang up in the elevators," said Dave Pericak, Mustang Chief Engineer.
"Like the team that did this in 1965, the current crew visited the Empire State Building before starting and took careful measurements of its new elevators and doors before cutting up the car."
The new Mustang is nearly 180mm longer and 100mm wider than its ancestor, making the task of transporting it up even more challenging.
Working from computer engineering data, team members preparing the display car have found just the right places to make the cuts so everything can be loaded onto custom-made racks that can be rolled into the lifts.
Once everything is transported up 86 floors, the technicians will have less than six hours to reassemble the sections into a complete car that will be on display above Manhattan.