The fly reel and the center pin reel share the same design concept and have quite obvious similarities.
They are, however, quite different, serving different fishing purposes of which there is no crossover.
Here are some key basic differences.
The first obvious difference is that modern center pin reels are generally much larger than fly reels. You will also find that it is rare to find an accessibly priced center pin.
While affordable fly reels are readily available, the price of a center pin can take your breath away.
The center pin reel has no drag system. Fighting a fish is done by varying hand pressure on the reel. An engaging and exciting technique every angler should experience.
A fly reel has a variable drag system like a spin reel or baitcaster.
Fly reels are fished using specialized fly fishing rods or various lengths and weights. A Center pin is traditionally fished with very long slow action rods of lengths from 11 to 14 feet.
A center pin has a clicker, i.e., a mechanism to stop the reel from turning backward, but it is never used when fishing, and only engaged for storage and transport.
The center pin is used almost exclusively for float fishing, and they are not cast like a fly reel. The fly reel is used exclusively for fly fishing, a style and technique that is indeed very old and specialized.