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Senpai (or sempai) generally means senior or mentor. By virtue, a senpai is older and has more experience than his junior/ protege termed as the kohai.
The senpai system is prevalent in Japanese schools and companies. In schools, younger students consider the upper classmen as their senpai. You can see the senpai system at work especially in sports and music clubs. The freshmen will be under the "mentorship" of an upperclassman. In companies, an entry-level employee will be placed under the responsibility of a senior member. Whether in school or companies, the senpai is expected to train and to guide his kohai, usually for a year. In return, the kohai is expected to respect and obey his senpai. The senpai and kohai relationship may last even after the mentorship term.
Since I'm a foreigner, I've never been actually under a senpai. But I saw how it worked in my schools and business classes. It may have its downsides but what I have seen, so far, are the good things about it.