Translation:When will he come?
It also accepts "when will he come", which sounds less awkward.
I guess the problem with "arrive" is that in English we could use it regardless of destination point. You can say "When will he arrive here". You can also say "when will he arrive there".
来る on the other hand is not similarly flexible in its useage. It's used specifically to indicate travel from somewhere else, to where the speaker is (or will be). The closest we have to that in English is "to come"
As a sidenote, 行く holds the direct opposite function: indicating travel to a destination away from the speaker, hence "to go".
...it's actually a little more complicated than that, but roughly speaking, that's the idea.
"To arrive" and "to come" are two different words in Japanese, much as they are in English.
"To arrive" is 着く (つく), and conjugates to 着きます in polite form. For example (たとえば) : 日本に着きます。 (To arrive in Japan).
"To come", as we know, is 来る (くる), which is an irregular verb (along with する/します) and conjugates to 来ます (きます). For example: 明日、(あなたは)学校に来ますか。(Will you come to school tomorrow?).
Think of 何時 as "when is it" so asking the time is like "when is it now?" And in this semtence "when is it he will come"... when thinking of Japanese sentences you have to think a bit more old English. Its not that simple, but it helps to get past the barrier of Japanese simply using words in a different manner than their closest english equivalent.
The "what time", I'm guessing. いつ is a more generic "when" that could also refer to days (as in, "he'll arrive on Tuesday") rather than specifically time. For that you want 何時（なんじ） Having said that, in actual conversation, if it's clear from context that you're referring to time, you could use either one.