Achieving microholes with dimensionally higher accuracy on the Ti-6Al-4V alloy using traditional machining techniques is challenging. Micro-electric discharge drilling (μEDD) has become a prominent machining technique in fabricating microholes. Though there are extensive applications of μEDD in producing microholes in difficult-to-cut materials, the appropriate tool materials and process parameters determine the process characteristics and accuracy. Because of the uneven machining and inadequate debris flushing, the technique is less productive and results in high overcut (OC) and hole taper (HT) for the microholes as well as poor material removal rate (MRR). Additionally, the rate of electrode wear affects hole precision. To address these issues, a rotating tool electrode set-up was used to drill microholes in Ti–6Al–4V alloy. The impact of three distinct electrode materials, copper (Cu), tungsten copper (WCu), and tungsten carbide (WC), as well as various process parameters, was investigated. The μEDD was accomplished by changing input process parameters, viz. voltage (V), capacitance (C) and tool rotation speed (TRS) and using Cu, WCu and WC tool electrodes to examine their influence on the process response variables such as MRR, TWR, OC, and HT. The experiments for each electrode were designed using a Taguchi-based L9 array, and the results were examined using Analysis of Variance (ANOVA). Capacitance was found to be the most significant electrical parameter in the μEDD of the titanium alloy. At 10,000 pF capacitance, the WCu electrode showed the highest MRR 0.009247 mm3/min, which was 6.11% and 21.92% higher than the Cu and WC electrodes. In contrast, the WCu electrode had the lowest tool wear rate (TWR) of 0.002033 mm3/min, which was 280.61% and 61.61% less than the Cu and WC electrodes, respectively. The WC electrode exhibited more accuracy by reducing the OC and HT compared to the Cu and WCu electrodes. The Cu tool electrode owing to its lower melting point and high thermal conductivity ensued in higher TWR than the WCu and WC electrodes. The used of rotary tool enabled a steady machining and proper flushing of debris. The impact of the tool materials and process variables on the surface quality of manufactured micro-holes was also explored using scanning electron microscopy (SEM) and energy-dispersive X-ray analysis (EDX). The WCu electrode showed higher carbon deposition on the hole surface than the Cu and WC electrodes.