Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including the closely related model system C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNAseq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata’s divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. Notably, among such genes were two transcription factors previously shown in C. elegans to be important for body size that are regulated by TGF-β signaling, whose downstream zinc-finger transcription factor SMA-9 also has evidence of lineage-specific selection in C. inopinata. C. elegans-specific ontology enrichment reveals genes with divergent developmental dynamics tend to be expressed in neurons and regulate behavior; they also include genes important for molting and body morphology. A comparison of such genes with previous C. elegans experiments reveals overlap with stress response, developmental timing, and small RNA/chromatin regulation. These results have identified candidate genes that will be further investigated to test their roles in cell size divergence and broaden our understanding of the genetic bases of body size evolution.