Electrochemical biosensor based on polypyrrole/La2O3 nanoparticles@snowflake-like Cu2S nanostructure composite and ds-DNA modified pencil graphite electrodes for detecting Idarubicin was fabricated. Display omitted •La2O3 nanoparticles@snowflake-like Cu2S nanostructure composite was synthesized.•An electrochemical biosensor was fabricated with new nanostructure.•The modified biosensor achieves sensitive detection of idarubicin at nanomolar level.•This strategy is extended to practical assays of real samples. Serious efforts have always been made to detect DNA molecules by fast, cost-effective, and susceptible instruments and clarify changes in DNA structure exposed to chemotherapy medicines. Accordingly, the present study endeavored to introduce a novel DNA biosensor fabricated by surface modification of pencil graphite electrodes using polypyrrole/La2O3 nanoparticles@snowflake-like Cu2S nanostructure composite, or PP/La2O3 NP@SF-L Cu2S NS composites, to detect ds-DNA molecules and Idarubicin (IDA). To prepare the proposed DNA biosensor, the ds-DNA was immobilized on the PP/La2O3 NP@SF-L Cu2S NS/PGE surface. IDA was detected electrochemically using differential pulse voltammetry (DPV). Subsequently, ultra-high sensitivity was reported for the biosensor of ds-DNA/PP/La2O3 NP@SF-L Cu2S NS/PGE towards the IDA so that the obtained limit of detection (LOD) was 1.3 nM with the linear range between 0.01 and 500.0 μM. The active reaction sites and admirable electrochemical activity associated with the nanocomposites were probably responsible for the excellent efficiency of the proposed biosensor, which accelerates electron transfer on the electrode surface and intensifies ds-DNA immobilization. The binding properties of IDA and DNA were investigated by molecular dynamic simulation (MDS), molecular docking (MD), and multi-spectroscopic analysis.