This paper establishes small ball probabilities for a class of time-changed processes $X\circ E$, where $X$ is a self-similar process and $E$ is an independent continuous process, each with a certain small ball probability. In particular, examples of the outer process $X$ and the time change $E$ include an iterated fractional Brownian motion and the inverse of a general subordinator with infinite Lévy measure, respectively. The small ball probabilities of such time-changed processes show power law decay, and the rate of decay does not depend on the small deviation order of the outer process $X$, but on the self-similarity index of $X$.