From the /r/Nootropics FAQ:
MODAFINIL WARNINGS
Modafinil in combination with Caffeine may greatly increase anxiety in some people, above what could be expected from either one. Don't try mixing them for the first time when you're already in a stressful situation or sleep deprived.
Modafinil may cause serious skin reactions, including erythema multiforme (EM), Stevens-Johnson syndrome (SJS), and toxic epidermal necrolysis (TEN) The FDA advises people to immediately discontinue and contact a physician if a rash or other hypersensitivity reaction occurs. Onset of SJS tends to not be immediate and may come several weeks after use of modafinil. -- Case Report The risk of SJS appears to be very small, in the range of about 1 in 200,000 patients, with no reported deaths.[76]
Modafinil may decrease the effectiveness of orally administered hormonal birth control for up to 1 month after final dose via CYP3A4/5 induction.[77][78]
Modafini may increase blood pressure.[81]
Modafinil can make staying awake for extended periods of time pretty easy. That doesn't mean it's safe to do so. Forgoing sleep can have serious health consequences.
For the vast majority of people it is well tolerated, a very small amount of people experience serious side effects and that is when you really should have used doctor supervision.
A large amount of people also report headaches. A lot of this is because you need extra hydration and people forget to drink enough water, but it is also reported in a significant amount of people with proper hydration.
Most worringly is the possibility of liver and cardiac side effects which you may not feel (except for in terms of increased blood pressure), and if you get it off the Internet you are unlikely to get proper testing done. These effects are very rare, but serious when they present themselves. If you have cardiac or liver issues to begin with I wouldn't try it without doctor supervision.
They make certain kinds of female birth control less effective if that applies to you.
A lot of people report headaches. Part of that is that you need to stay very well hydrated, but it is also reported by a significant amount of people with proper hydration.
Then there is the laundry list of nausia, diarrhea, etc. that comes with pretty much any prescription medication but is very rare.
For the vast majority of people it seems to be either side effect free, or have headache as the only side effect.
It should also be noted that it is considered a performance enhancing substance so if you do competitive sports make sure you read the doping rules before starting. It is not detected by standard corporate drug screening policies. You pee will start to smell somewhat though which is fun, but if you often use communal bathrooms and wish to keep your modafinil usage secret can be a bit of a problem.
Another side effect which is not widely reported is that it makes you poop. Not immediately but like large doses of coffee it tends to induce your digestive system to get motivated. This should especially be noted if you take it before going out or before attending a several hour exam. People seem to have this to varying degrees, but if I take a 200mg dose (regular dose) I can guarantee a visit to the toilet in the next 10 hours as long as I've eaten something that day.