Sumeet is married to Radhika; they want to have child but run into sexual problems. They go to Dr. Sangeeta who runs tests on both and finds that results are all fine. She discusses the problem with them. Apparently, Sumeet faces problems during sex because of a past history. Dr. Sangeeta advises Radhika to take corrective steps. The solution works and the couple's treatment is successful.
While Sumeet and Radhika seem to have solved their problems Sumeet's brother, Hrithik, studies in collage and fall in love with Dr. Sangeeta's sister, Prachi. They have an intimate relationship and Prachi gets pregnant. Instead of going to her doctor-sister for help, Hrithik seeks advice from a friend who gets him a pill to give to Prachi to abort her pregnancy. However, after she takes the pill, Prachi bleeds to death, proving that it would have been better for the couple to seek professional help in terminating the pregnancy.
Secret Of Sex purports to be a sex education film, tackling simple problems and offering simplistic secret solution.