Purpose: To compare the electron beam (EB) characteristics of two Elekta™ linear accelerator (LINAC) models having significantly different treatment head designs. Method and Materials: An Elekta™ Synergy™ LINAC and a Synergy‐S™ (Beam Modulator™) are in clinical use at our institution. The Synergy™ treatment head design replaced upper jaws with 40 MLC leaf pairs (1‐cm wide projection at isocenter) followed by a backup diaphragm parallel to MLC leaves; lower conventional jaws are perpendicular to the MLC. Maximum field size at isocenter is 40cm×40cm. The Synergy‐S™ treatment head design replaced both upper and lower jaws with an 80 leaf (40 each side, 0.4cm leaf width at the isocenter) Beam Modulator™ and two pairs of fixed outer diaphragms. Maximum field size projected at isocenter is 21cm×16cm. Electron applicators are attached directly to the treatment head on both machines. A Wellhöfer™ blue water phantom system was used to measure and compare EB PDD, off‐axis profiles and output factors for all EB energies on both machines at several different SSDs. Depths used for profile measurements were (1/2)R90, R90, R70, R50 and Rp+2cm. Field sizes for the output factor measurements are ineer, compromises were required to meet both PDD and flatness specifications. Synergy‐S™ EBs were higher energies (as shown by PDDs co2cm2–10cm2. Results: While beam energy matching was attempted by the eng mparisons) for same nominal energies. Off‐axis profiles for Synergy‐S™ were more rounded than Synergy™. No significant difference between in‐line and cross‐line profiles was noted for either machine. Bremsstrahlung properties of both machines are similar. Output factors for fields defined with 6cm2 applicator of Synergy‐S™ are about 4% higher. Conclusion: Electron beam characteristics of Synergy™ and Synergy‐S™ are significantly different. Special caution should be taken when using the treatment planning beam model for one system to estimate the dose distribution for the other system.