There are two things that you need to implement such a system: a list of activities and their caloric costs per unit time, tailored to the age and weight of the character; and a list of the caloric values of various foods. A ready-made system for roleplaying games doesn't appear to exist, but given the mass of information out there for dieting and body-building purposes, such tables merely need to be compiled. Building such is beyond the purpose of a Q&A site, so I'm just providing the basic pieces below.
There is this daily calorie intake calculator to start with. It doesn't break down exercise beyond how many days out of seven and how much exertion (default vs "intense"). However, punching in weight, height, age, and 7-days-a-week of intense exercise would give you how many calories per day are required to maintain the current physical state. For example, punching in my numbers indicates that, were I an adventurer slogging through swamps and swinging four pounds of steel to save my life, I would need to consume up to 3597 calories per day of full-on adventuring, and about 1200 calories less on days of rest and relaxation.
To get more detailed, you could look at the calculation methods, as used by dietitians, that underlie these online calculators. The above online calculator offers three equations by name:
There are also caloric cost calculators online for specific activities. This Calories Expended site gives a drop-down of many activities, to which you can add the time spent and the body weight moved to find the calories used. You can probably find analogues for the various activities and adventurer might undertake in that list. You could use that calculator to find the cost of all activities in a day, and use the calories-required equations above as a "sanity test" to keep the numbers approximately correct.
The final piece of the puzzle is a list of foods and the calories they can provide. The Calorie Counter has extensive lists of foods and their typical caloric value. Although finding exact matches for foods in historical/fantasy settings is unlikely and would probably take some guessing to find approximate matches, for a more modern-day game the list should be spot-on.
Given those pieces, it should be possible to weld together a working system akin to the one in Cryptonomicon.