I had been having a headache, so I will not attend the meeting.

The second part of the sentence uses the future simple tense, while the underlined part uses the past perfect continuous. These two do not logically connect and clash temporally. The first part should therefore use a present tense, which naturally leads to a future consequence. Secondly, the article is missing with the word "headache". It should be "a headache"

The correct sentence should therefore be: I have a headache, so I will not attend the meeting.

This matches with option C, hence C is the correct choice.