If your body fat percentage is 20 or higher, you probably are skinny fat, like me. When I say 20%, I mean 20% as measured by a DEXA scan. (Most people dramatically underestimate their body fat percentage.)
I am a 48-year old man. I've been running off and on for about 40 years. My PRs in college were 16:04 for the 5K and 33:57 for the 10K. I can't run anywhere near those times today. My current body fat percentage is 23 percent (confirmed by DEXA scan). This is an improvement from a few months ago when I was at 27 percent. I am currently 5'11, 165 pounds.
Here's some advice for my fellow skinnyfat hobby joggers:
1) You are eating too much. You may think you don't need to worry it because you are a runner, but your post-run gatorade (80 cal), bagel with cream cheese (440 cal), and frappucino (170 cal) canceled out that 7-mile run you just did. Here are some hard truths: (1) it is almost impossible to run your way out of a bad diet and (2) it is much easier to cut calories than to run more. Relatedly, you need to learn the difference between physiological hunger and psychological hunger (stemming from boredom, habit, or whatever). True physiological hunger is pretty rare.
2) You are eating too many carbs and too many refined foods. At the end of the day, of course it's all about calories in and calories out. But some foods (e.g., salmon, chicken, broccoli) reduce hunger more than others (e.g. pasta, pancakes) for a given number of calories. So look into a Paleo low-carb diet.
3) You are eating too often. If you want to lose weight, limit your eating window to a short window each day (intermittent fasting). A low-carb diet and intermittent fasting work extremely well together.
4) You are weak. To reduce your body fat percentage, build muscle. Lift heavy. Do compound movements such as squats, deadlifts and bench press. Pay a Personal Trainer to make sure your form is good. You will get stronger. You will look way better and feel better and you will much be less susceptible to injury. Whether your times will drop is an open question, but (seriously) there is more to life than getting faster.