Yes, it mean "the train leaves / will leave in a while". We use で for "in" of "in + quantity of time", for example: We will arrive at your home in an hour. = 一時間であなたの家につきます。 It's like "(We have) an hour to arrive at your home" though it would sound weird in English. I have to finish my work in 10 minutes. = 10分で仕事を終えなければなりません。 You can also use this で for money. You can buy this and this in 5 dollars. = 5ドルでこれとこれが買えます。 I hope you got it.