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First of all, I realize that when traveling to another state for employment it is commonplace to owe taxes in that state for the work performed+sourced in that state.

Example: you work/live in Pennsylvania but travel to do work on-site at a facility in California two months. California is entitled to collect income tax on your annual income * 2months/12months per California tax law.

My question pertains to alternate situation where the trips are much shorter and thus the fractional time spent in transit becomes significant.

Example: Live in Colorado but fly to California every single week on Tuesdays and returning on Thursdays. Working from Colorado Mondays and Fridays.

It is clear that 2/5 of the time is spent working in Colorado (Monday/Friday). Furthermore, 1/5 of the time (Wednesdays) is spent wholly in California. On Tuesdays and Thursdays, some work is performed in Colorado and some work is performed in California. But, a significant amount of time is spent in transit (e.g. 50%).

Is there a precedent set as to which state taxes are owned during a transit day? In this particular case, it could amount to a difference in taxes of thousands of dollars annually.

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Just a guess here, and maybe it's under a wrong assumption:

Since the travel time is only related to work done in California, the travel expense and your paid work time spent in travel would be taxable in California.

I would not count the travel time income/expenses with regard to taxes in your state of residence.

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