Both forms are possible, but there is a slight difference in meaning. "Meeting with someone" normally refers to a pre-arranged meeting to discuss a specific issue. My impression is that this form is more common in American English than British English.
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Manjunath ShenoyIt was a pleasure meeting youUse this one when you finish your conversation after meeting someone for the first time.
Manjunath ShenoyIt was a pleasure meeting with youUse this one when you finish the (business) meeting you previously arranged with that person (or with those people) -- if you'd like. This