Answer by Bart Loews:

There’s a lot to talk about here.
A quick discourse on energy systems:
This is a bit of an oversimplification, but you have 2 main energy systems that you’re looking at when you’re running, your anaerobic energy system (your glycogen or stored sugar), and your aerobic energy system (your fat stores). The primary system that keeps you going is aerobic glycolysis. While you can function for short bursts anaerobically, the metabolic process actually costs your body 4 ATP molecules (6 in your liver are spent converting lactate to glucose, and only 2 ATP are created in the muscles).  With oxygen in the equation, the Krebs cycle can generate 32 ATP molecules (which is why you breathe so much). [Aerobic vs. anaerobic glycolysis]
You always use both systems, when you’re at rest you primarily use your anaerobic energy system. Your anaerobic energy system is far more accessible for your body to use, it doesn’t require oxygen to access the energy.  Aerobic energy does require oxygen. The longer you keep up an activity, the more you use your aerobic energy system over your anaerobic system.
Fat is the least accessible form of energy, but it lasts you the longest.
To directly burn fat, you need to run for at least half an hour to really kick off your aerobic energy system.
The longer you run the more fat energy you’ve burned off.  But there’s more to it than just that.
Moderate paces will use your fat stores more, which is where zone theory comes into play.  If you run between 55% and 75% intensity you’ll live in the “fat burning zone” which is a bit of a myth.  Yes, you’ll be burning fat more readily than sugar while you’re running, but you’re actually getting a terribly inefficient workout at the cost of your muscles.  If you’re training for a marathon or iron man, this can be good for you, you’ll build up your aerobic energy systems for more bandwidth and accessibility. For actual fat loss it’s counter-intuitively not good for you.
Your best bet is to run in a cardio and anaerobic zone.  This will make your anaerobic endurance better, which is good for relatively short bursts of energy.  More importantly it’ll work your muscles and bones more, causing them to grow a stronger and thicker.  Further, the harder you work, the more Exercise Post Oxygen Consumption (EPOC) you’ll experience.  The more EPOC, the more calories you’ll burn after a workout.
The most effective way to get EPOC is to do interval training.  Run very hard for an interval and then run easy for an interval. Run hard, run easy. You could also sprint, walk, sprint, walk.  Try to keep the intervals even.  The more you can do, the better.
Dr. Tabata broke his speed skaters into two groups. One group he did interval training with for 4 minutes (20 seconds at 100%+, 10 seconds rest for 8 sets) after a warm up followed by a cool down.  The other group he did steady state cardio for an hour.  The interval group saw marked improvement in their anaerobic endurance versus the steady state group.  In just 4 minutes.  Now, there’s benefits to doing steady state cardio, but to lose fat, you’d be best off working your anaerobic systems.  I’d recommend far more than 4 minutes, aim for at least 30 to really kick things into gear. Tabata’s goal was anaerobic fitness, not weight loss.  A final note, with High intensity interval training, you need to really kick it into high gear.  Go all out, especially at the end of the work out, you get the most out of it when you’re already tired.
There’s no guarantee you won’t lose muscle. To limit muscle loss you should do your cardio along side weight lifting and be sure to get enough protein and carbs, but not too much (it’s a very careful balance, something most people can’t easily accomplish).  Usually people will bulk up, then cut down. In the cut down process they’ll lose some muscle, but mostly fat.  It’s possible to do both, but it’s pretty stressful. The best recommendation for building muscle and losing fat I’ve seen, numbers wise is a modified ketogenic diet with caloric deficit. To do that, you’d definitely need more stimulus through weight lifting. HIIT might get you some leg muscles, but your upper body will suffer.

What can I do to improve my running performance?