In deep-hole electrical discharge machining, the exclusion of debris is difficult, which leads to debris stagnation in the side gap. Thus, the wall of the machined hole becomes concave owing to secondary discharges in the side gap, even with the use of a linear-motor-driven EDM system with high-speed electrode jump. In this paper, the EDM of a deep hole using a flange-type electrode is proposed in order to prevent secondary discharges in the side gap and to improve shape accuracy. The EDM characteristics such as shape accuracy, removal rate and surface roughness are compared between the use of a flange-type electrode and that of a conventional straight electrode. The fluid flow and debris movement around the flange part of the electrode during the electrode jump are also discussed in view of the results of high-speed camera observation and CFD analysis. In addition, the effects of electrode shape on hole shape are investigated. Experimental results show that the concavity of machined holes can be easily improved using a flange-type electrode, even when using a conventional EDM with a ball screw drive. EDM performance becomes stable with the use of a flange-type electrode, and consequently removal rate improves.