Taking clomifene in the second day of menstruation can stop the period?

It shouldn't. . Clomid (clomiphene) is used to help infertility caused by chronic annovulation. It shouldn't alter your period a whole lot. That being said, typically, patients start Clomid (clomiphene) on cycle day 3. Check with your physician to see what day he/she wants you to start. Best of luck to you!