A QCD from a SEP IRA is allowed as long as it is not an on going SEP IRA per Notice 2007-7, Q 36 copied below. If the SEP is “on going” according to the definition, then a direct transfer from the SEP to a TIRA would allow the QCD and RMD to be taken from the TIRA using the RMD aggregation rules. A 60 day rollover to the TIRA would not work because any distribution from an IRA in an RMD distribution year is deemed to apply to the RMD. Normally, the QCD should be done first so the RMD is offset by the QCD. Of course, if the RMD is much larger than the QCD, then the timing can be altered as long as there is enough RMD remaining for the QCD to offset the remaining RMD.

Q-36.  Is the exclusion for qualified charitable distributions available for distributions from any type of IRA?  A-36.  Generally, the exclusion for qualified charitable distributions is available for distributions from any type of IRA (including a Roth IRA described in § 408A and a deemed IRA described in § 408(q)) that is neither an ongoing SEP IRA described in § 408(k) nor an ongoing SIMPLE IRA described in § 408(p).  For this purpose, a SEP IRA or a SIMPLE IRA is treated as ongoing if it is maintained under an employer arrangement under which an employer contribution is made for the plan year ending with or within the IRA owner’s taxable year in which the charitable contributions would be made.

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