Sex determination is a critical developmental decision with major ecological and evolutionary consequences, yet a large variety of sex determination mechanisms exist and we have a poor understanding of how they evolve. Theoretical and empirical work suggest that compensatory adaptations to mutations in genes involved in sex determination may play a role in the evolution of these pathways. Here, we directly address this problem using experimental evolution in Caenorhabditis elegans lines fixed for a pair of mutations in two key sex-determining genes that jointly render sex determination temperature-sensitive and cause intersexual (but still weakly to moderately fertile) phenotypes at intermediate temperatures. After 50 generations, evolved lines clearly recovered toward wild-type phenotypes. However, changes in transcript levels of key sex-determining genes in evolved lines cannot explain their partially (or in some cases, nearly completely) rescued phenotypes, implying that wild-type phenotypes can be restored independently of the transcriptional effects of these mutations. Our findings highlight the microevolutionary flexibility of sex determination pathways and suggest that compensatory adaptation to mutations can elicit novel and unpredictable evolutionary trajectories in these pathways, mirroring the phylogenetic diversity, and macroevolutionary dynamics of sex determination mechanisms.