One question that I get asked on The Peak Testosterone Forum is how long it takes for Clomid to get out of your system once you stop taking it. This issue comes up fairly often for several reasons: a) some men do not respond well to Clomid and their testosterone does not increase much, b) some men experience significant side effects with Clomid, such as headaches, floaters, moodiness, lowered libido, depression, etc. and c) still other men only wanted to use Clomid temporarily and then wish to try out standard testosterone. therapy
Regardless of the reason, Clomid can take awhile to clear out of system and for any side effects to withdraw. The reason for this has to do primarily with the half life of one of the isomers in Clomid. Clomid is actually composed of two different drugs, enclomiphene and zuclomiphene. The former actually has some anti-estrogenic effects and has been the subject of considerable press lately, because it is the sole active ingredient in Androxal. You can read more about this in my page on Testosterone and Androxal if you are interested. (It is still awaiting FDA approval as of this writing in Dec. of 2015.)
The other isomer is zuclomiphene and it is primarily responsible for Clomid's estrogenic properties. As such, this is the isomer that is most of interest when it comes to figuring out the time for Clomid to "clear out of your system." And, unfortunately, zuclomiphene has the longest half life - significantly longer - and this is why estrogenic side effects can linger for quite awhile after quitting Clomid. So what is the half life of these two isomers in Clomid? This question was probably most definitely answered in a study on women. 
|Half Life (Days)||Half Life (Days)|
As you can see the zuclomiphene half life is 3-5 times longer than the enclomiphene. The authors point out that you will start out with more enclomiphene in your system, but, somewhere between 1 and 7 days, zuclomiphene will take over.
So how long does the zuclomiphen take to clear out of one's system? One of our senior posters (seppuku) had an interesting story that his testosterone was still boosted three weeks after just a few small (and low) doses of Clomid:
"A few years ago when I was going through the nhs system of blood tests and hopeless endos, I'd got hold of some clomid and had taken two 12.5mg doses during a week. I then got a letter from the hospital to see the endo in about three weeks. So of course I took no more clomid thinking it would be having no effect by then. He took a blood draw, and my usual level of around 290 - 340 had gone up to I think around 450ish. So the longer you can leave it the better, six weeks sounds reasonable." 
So seppuku's theory was that six weeks is about right for the time to clear it out of your system. Is that correct? Actually, that seems like a very reasonable number based on what I seen here:
NOTE: Most men can boost their testosterone nicely with Clomid, which is an indication that most men have tertiary hypogonadism, i.e. it is centered in the hypothalamus as opposed to the pituitary or testes. For more information, see my page on Clomid and Testosterone.
"Importantly, unlike clomiphene citrate, letrozole is devoid of any anti estrogenic peripheral action. Letrozole is also cleared from the circulation more rapidly due to a shorter half life (48 hours) as compared to clomiphene citrate which may take up to 2 months due to its prolonged half life (2 weeks)." 
Therefore, based on this study (on women), six weeks is not unreasonable, but it can be even longer - up to two months. And this is reasonable, because usually it takes about four to five half lives to be completely out of your system. In the case of the second woman, this actually works out to be three months or more! Practically speaking, I don't think it usually takes that long.
What is a reasonable way to tell if it has cleared from your system? Well, one way is to look at when you return to your testosterone levels, assuming you have a total testosterone read from before you started the Clomid. By the way, in small percentage of men, Clomid can be a way to "reboot" to normal and healthy testosterone levels. See my on Testosterone Restarts for more information.
1) British Journal of Clinical Pharmacology , May 1, 1989, 27(5), "Pharmacokinetics of intravenous clomiphene isomers"
3) Reprod Biol Endocrinol, 2011; "Letrozole or clomiphene citrate as first line for anovulatory infertility: a debate"
4) Fertil Steril, 1999 Apr, 71(4):639-44, "Serum concentrations of enclomiphene and zuclomiphene across consecutive cycles of clomiphene citrate therapy in anovulatory infertile women"