“There is also the judgement of God, who encounters us and says to us at every moment, ‘This is not enough.’ I may even reach the point of asking myself, ‘Underneath it all, am I a Christian? My faith being small and my obedience slight, of what meaning are these words: ‘I believe, I obey’? Deep is the abyss. The core of our being is put to question at the very moment we believe and obey as well as we can. In this situation (which is the same for every Christian) prayer means going toward God…
“Prayer means that we address ourselves to God, who has already spoken to us in the gospel and in the law. We find ourselves face to face with him when we are tormented by the imperfection of our obedience and the discontinuity of our faith. Because of God we are in distress. God alone is able to heal us of it. In order to ask him to do so, we pray”
(Karl Barth, Prayer, 10-11. Westminster/John Knox Press, 2002)
“Help thou mine unbelief” is always a prayer. (Important that it is not a statement, a question, a treatise, but an address, a plea, a prayer.) In the face of suffering, the natural (possibly the only) response, if we are honest with ourselves, is unbelief. What kind of God would allow such suffering to exist? How can God be love if these things happen? The natural world, as we see it, cannot give us a consoling answer to these questions. We cannot, given the enormity of suffering in the world, overcome it through logic, or through our own ability to believe. Faith and trust and belief are the least natural responses. That is to say, they only exist as miracles, as gifts from God, and always (while we are alive in this world) in a mixed form. Belief and unbelief, etc.
We can’t overcome our own unbelief. It is too strong. (Even the disciples did not have enough faith in this case. cf Mark 9:14, ff). Only God can help our unbelief, and that is why we pray, Help thou mine unbelief.