The small cabbage butterfly, Pieris rapae, is an important pest of cruciferous corps, and Pteromalus puparum is a predominant pupal endoparasitoid wasp of this butterfly. For successful development of parasitoid offspring, female parasitoids usually introduce one or several kinds of maternal factors into the hemocoels during oviposition to suppress host immunity. To investigate the early changes in host immune‐related genes following parasitization, we analyzed transcriptomes of parasitized and unparasitized, control, host pupae. Approximately 17.7 and 19.3 million paired‐end reads were generated from nonparasitized and parasitized host pupae, and assembled de novo into 45,639 transcripts and 27,659 nonredundant unigenes. The average unigene length was 790 bp. A total 18,377 of 27,659 unigenes were annotated and we identified 557 differentially expressed unigenes in host pupae at 1 h after parasitization, of which 21 were immune‐related. Parasitization led to downregulation of most pattern recognition receptors and upregulation of all serine protease inhibitors. The transcirptomic profile of P. rapae is considerably affected by parasitization. This study provides valuable sources for future investigations of the molecular interaction between P. puparum and its host P. rapae.