What is energy output in Strava application?
From Strava's Help page :


  Energy Output
  
  Energy Output measures the amount of work you've done during a ride,
  expressed in kilojoules (KJ). It is a factor of how much you're
  pedaling, how fast you're pedaling and how much force you're exerting
  on the pedals (measured in W). Power output is most accurately taken
  from a power meter, but if you don't have a power meter we give a
  rough approximation through our power estimator.


This means how much energy was delivered to make the wheels turn. As Daniel R Hicks mentioned, calories in that case mean how much "food" energy your body burned, which will always be higher than the energy you give to the wheels.