Yes, if the taxpayer qualifies for Form 2555, you would fill that out in ProSeries.

I don't remember if the 2555 has a way to 'flow' to the wages on Form 1040 or not, if but not, you enter the foreign wages on line 1h of the 1040 (click that box a few times and it will give you a worksheet, and one of those lines is for foreign income).

The 2555 becomes part of the 1040.

The foreign tax credit , if tax is paid to Japan, might give a better tax result. Run it both ways.

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@imantax wrote:

the W-2 has been translated. 

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You can't rely on the Gensen to determine the amount to report for US tax purposes because the two jurisdictions have different tax rules.  Instead, you need to review each item of compensation and benefit, whether or not it is subject to Japan tax in part or in full, to assess the proper US tax treatment.  And that includes any NQDC that needs to be tracked and managed to mitigate §409A exposure.

You may also have to grapple with foreign pension that are nonqualified under US tax law, which could then also give rise to foreign trust issues, PFIC's, etc.