We study the deformation theory of rational curves on primitive symplectic varieties and show that if the rational curves cover a divisor, then, as in the smooth case, they deform along their Hodge locus in the universal locally trivial deformation. As applications, we extend Markman's deformation invariance of prime exceptional divisors along their Hodge locus to this singular framework and provide existence results for uniruled ample divisors on primitive symplectic varieties which are locally trivial deformations of any moduli space of semistable objects on a projective K3 or fibers of the Albanese map of those on an abelian surface. We also present an application to the existence of prime exceptional divisors.