MnO2 nanorods incorporated MCM‐41 nanocomposite (MnO2@MCM‐41) is synthesized and employed as an electrode modifier for individual as well as simultaneous detection of purine bases, guanine (GU) and adenine (AD). For this purpose MnO2 nanorods are encapsulated within MCM‐41 by simple one pot synthetic approach. FT‐IR, UV‐vis absorption spectroscopy, scanning electron microscopy, energy dispersive X‐ray spectroscopy, X‐ray diffraction, X‐ray photoelectron spectroscopy and electrochemical methods are employed to characterize the nanocomposite and other materials. The electrochemical attributes of glassy carbon electrode (GCE) modified with the MnO2@MCM‐41 (represented as GCE/MnO2@MCM‐41) towards the determination of GU and AD is studied in detail. Upon incorporation of MnO2 nanorods on MCM‐41, noticeable upsurge in anodic peak current with a decline in peak potential is observed for both GU and AD oxidations in cyclic voltammetry studies. Individual as well as simultaneous determination of GU and AD are performed using differential pulse voltammetry (DPV) technique which offered a linear range of 100 nM to 100 μM for GU and AD with respective limit of detections, 44 and 66 nM. The practical applicability of the GCE/MnO2@MCM‐41 for real world samples analysis is satisfactorily demonstrated with certain DNA samples by DPV.