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Is this the outside (pinky toe), or the inside (big toe)?
Any pain elsewhere in the lower back, thigh, calf/shin?
How about the inside of the ankle?
Tarsal tunnel may be one possibility here:
where pressure on the nerve can cause pain into the bottom of the foot.
Also, it could be S1 nerve irritation coming from the lower back:
although that also tends to cause lower back and leg symptoms, as well as the bottom of the foot type pain.