If we have an employee that on his final check wants to pre-pay his cobra payments could that be considered a pre-tax deduction?

Off-hand, I see no reason why not.

Because payment of his share of the medical insurance is a pre-tax deduction, by logical extension his payment of the COBRA medical costs can also be treated as a pre-tax deduction unless it is specifically prohibited by the tax law which made employee medical inusrance payments tax-deductible.

Atlanta: I've seen many of your posts and an impressed with your knowledge. I have a couple of thoughts on this. See if they make sense to you.

When we say COBRA, we're usually thinking the medical insurance aspect, but there is also the Flexible Spending account part, for those who have that. The Flexible Spending Account would give a way to handle post-employment COBRA medical insurance cost, if the employee is eligible to continue Flexcomp coverage and hasn't already expended the limit for the year. The contribution could be made to the Flexible Spending Account (Life changing event, i.e. termination, being justification for changing the contribution amount. This would only handle the COBRA medical insurance costs for the rest of the calendar year though.

For someone without Flexcomp, it is true that the employee share of medical insurance premiums is a pre-tax deduction while employed. But, insurance premiums paid by unemployed persons are a deductible medical expense subject to the 7.5% of AGI limitation. I don't see how prepayment of the premiums could change this. And, COBRA medical insurance normally is applicable for 18 months and under some circumstances, double that. Certainly, only premiums for the remainder of the current year are at issue.

So, all that leads me to the conclusion that the pre-payment would not be a pre-tax deduction on the final check, but would be deductible on Schedule A subject to the 7.5% limitation.