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I've tried the intersect function but that also returns small zipcodes entirely within a city. Ideally, I just need zipcodes that extend beyond city lines.

atlasofcoffee
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The tool you are looking for is select by location under: Vector => Research Tools => Select by Location with settings as in the image below.

enter image description here

The zipcode layers goes in the first dropdown and the city layer in the second dropdown. Check include features that overlap/cross the selection features. And you should get only intersecting features as below:

enter image description here

ZrSiO4
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  • I have QGIS 2.18 and the window looks completely different. The issue I have is I know multiple zipcodes are in multiple cities and vice versa. Is there a way to do a many to many join? – atlasofcoffee Nov 22 '17 at 21:20
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    I used QGIS 2.14.14 for the screen shots... And I think the discussion on this link may be helpful to resolving you question: https://gis.stackexchange.com/questions/53918/determining-which-us-zipcodes-map-to-more-than-one-state-or-more-than-one-city – ZrSiO4 Nov 22 '17 at 22:15