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My friend got a visa to travel to Japan from the Japanese Embassy in Nepal. Instead of boarding from Nepal ie Kathmandu Airport, he wants to board from India ie Delhi to come to Tokyo.

Is that OK, or does he need to board from Nepal only?

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It's fine. Visas are for the country you are going to, not the country you are coming from.

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In particular, it's very common for there to be few or no direct flights from country A to country B, which means that it's often necessary to travel via some third country. – David Richerby Feb 23 at 15:50
Consider also tours requiring multiple visas. – Patricia Shanahan Feb 23 at 17:58

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