You should think about WHY it's uncomfortable. Is is the correct size frame? Is it because the seat is uncomfortable? Do you get pains in your arms? elbows? wrists? knees? Are you carrying things in a backpack instead of having weight supported by the bike while you are riding? (get saddlebags). Those answers will start to tell you what is not properly adjusted. The reason to get a used bike is to understand these things.
The other question is: What city and how? Riding the greenway of Anchorage, Alaska is a whole lot different from the roads of San Francisco. Are you looking at a road bike or a hybrid? Is the bike you have the same style (same seat shape, handlebars, et al?). If you are changing a lot of variables, I would recommend getting a used bike closer to what you think you want. If what you're thinking is already close to the uncomfortable one you have, then you can decide if new is worth it (and also if new will solve your issues with the bike)
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Still learning this side, credit on the above to the prev poster...
I bike quite a bit (road bike, long distance) and the above comment nailed it. Also realize your body will need time to adapt to biking (minor sore legs, butt... the first few rides after not riding for several months is normal). Either pay or learn how to set the bike up for you, assuming it's the correct size, learn how to fix a flat (and carry to tools to do so), and get riding!