Learn English – Should an exact time come before a day when specifying when something will happen

Both sentences are 'correct' but typically when there are multiple time adverbs in the same utterance the more specific comes before the less specific.

At 9.45 is a more specific time than tomorrow morning so this typically comes first:

It will leave at 9.45 a.m. tomorrow morning .

Collins Cobuild English Grammar (p266) in the section ordering of time expressions states:

... the usual order is clock time, followed by the period of the day, day of the week, and date.

• at eight o'clock on the morning of 29 October 1618
• on the night of Thursday July 16

The alternative word order:

It will leave tomorrow morning at 9.45 a.m.

is just as grammatical, and may be preferred if 'tomorrow morning' is the more important information than the clock time.