Here's a compilation of some of the answers given in comments.
As pointed out by Mark Sapir and Misha, if $S$ is a compact surface with one boundary component whose fundamental group is equipped with an isomorphism $\alpha : \pi_1(S) \to F_n$, and if $f : S \to S$ is any pseudo-Anosov homeomorphism, then the outer automorphism of $\pi_1(S)$ induced by $f$ ($\leftrightarrow$ the mapping class of $f$) pushes forward via $\alpha$ to give an outer automorphism $\phi$ of $F_n$ whose only periodic conjugacy classes are those associated to the boundary component of $S$. So for any automorphism representing $\phi$, all of its fixed points are in the commutator subgroup. And one can easily construct such a pseudo-Anosov $f$ which is in the Torelli subgroup of the mapping class group of $F_n$: apply Penner's recipe, taking two filling, separating curves $c,d$ and composing a positive Dehn twist about $c$ with a negative Dehn twist about $d$. The (outer) automorphism of $F_n$ induced by such an $f$ is in $IA_n$.
But from those examples, one can construct further $IA_n$ outer automorphisms whose only periodic conjugacy class is the identity. To do this, pick two isomorphisms $\alpha_1,\alpha_2 : \pi_1 S \to F_n$ taking the conjugacy class represented by $\partial S$ to two distinct conjugacy classes in $F_n$. Let $\phi_1,\phi_2$ be the two $IA_n$ outer automorphisms of $F_n$ obtained by pushing $f_*$ forward via $\alpha_1,\alpha_2$ respectively, so their fixed conjugacy classes are distinct from each other. Then for high powers of the exponents, the $IA_n$ outer automorphism $\phi_1^i \phi_2^j$ has no periodic conjugacy class at all; this is a consequence of Theorem 1 of this recent preprint of Pritam Ghosh.