We give an efficient algorithm to randomly generate finitely generated subgroups of a given size, in a finite rank free group. Here, the size of a subgroup is the number of vertices of its representation by a reduced graph such as can be obtained by the method of Stallings foldings. Our algorithm randomly generates a subgroup of a given size $n$, according to the uniform distribution over size $n$ subgroups. In the process, we give estimates of the number of size $n$ subgroups, of the average rank of size $n$ subgroups, and of the proportion of such subgroups that have finite index. Our algorithm has average case complexity $\O(n)$ in the RAM model and $\O(n^2\log^2n)$ in the bitcost model.