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Just to clarify, why would you pay 3.5 months of N.J. state taxes in the 1st place? Did or didn't your employer withhold any taxes in NJ for that pay period in the first place?  From what you are telling me now, it seems like he didn't withhold any NJ tax so where does the 3.5 months come into play?  

 

Once again, you will be paying two weeks worth of tax for the amount of time spent in NJ as a part time resident and the remaining time spent in NY as a part time resident. Any additional withholding tax that your employer took from you as a NY resident which in your case would be two weeks will come back to you as an additional  refund or a reduction in your total tax liability for NY.  

 

Whatever the calculation is for the state of NJ, namely the two weeks that you resided there, is what it is. If there indeed was 3.5 months worth of NJ withholding tax, then once again come back to you as an additional refund or as a reduction in your total tax liability for NJ.

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