I often see these two words used interchangeably.

Problem:
These two nouns are not synonyms.

Explanation:
Identical pronunciation of these two nouns makes them homophones, as noted at Wikipedia.

The word “calorie” — with a lowercase “c” — means an amount of heat equal to 4.184 joules.

In case you do not remember your basic physics, one “joule” refers to the work done by a force of one newton acts through a distance of one meter or to the current of one ampere passed for one second through a resistance of one ohm.

The word “Calorie” — with a capital “C” — means 1000 calories (with a lowercase “c”), also known as a “kilocalorie” (also with a lowercase “c”).

The common English blunder is to write “Calorie” — with a capital “C” — as “calorie” — with a lowercase “c” — when referring to the energy value of a food item.

For example, a “2000-calories-per-day diet” — with a lowercase “c” — would provide almost no energy and might have been suitable for Mahatma Gandhi when he was on a hunger strike.

Aside: I recently saw a beautifully shot movie titled “Water” that weaves Gandhi into a story set in India. The story was fascinating and touching, and the acting was excellent. I highly recommend it!

In contrast, a “2000-Calories-per-day diet” — with a capital “C” — would be on the order of magnitude of what many adults require to maintain their body weights.

Solution:
Remember that capital “C” is larger than lowercase “c”, just as “Calorie” with a capital “C” is larger — in fact, one thousand times larger — than “calorie” with a lowercase or small “c”. When referring to the energy value of food, use “Calorie” with a capital “C”.