Cyclin dependent kinase 9 (CDK9), a key regulator of transcriptional elongation, is a promising target for cancer therapy, particularly for cancers driven by transcriptional dysregulation. Here, we report the characterization of NVP-2 (3), a selective ATP-competitive CDK9 inhibitor; and THAL-SNS-032, a selective CDK9 degrader consisting of a CDK-binding SNS-032 ligand linked to a thalidomide derivative which binds the E3 ubiquitin ligase Cereblon (CRBN). Surprisingly, THAL-SNS-032 induces rapid degradation of CDK9 without affecting the levels of other SNS-032 targets. Moreover, the transcriptional changes elicited by THAL-SNS-032 were more like those caused by NVP-2 than those induced by SNS-032. Strikingly, compound washout did not significantly reduce levels of THAL-SNS-032-induced apoptosis, suggesting that CDK9 degradation had prolonged cytotoxic effects compared to CDK9 inhibition. Thus, our findings demonstrate thalidomide conjugation represents a promising strategy for converting multi-targeted inhibitors into selective degraders, and reveal that kinase degradation can induce distinct pharmacological effects compared to inhibition.