A new ⁹⁰Sr/⁹⁰Y catheter-based system, the Beta-Cath 3.5F system, was recently introduced into the clinic for intravascular brachytherapy. This new system has a smaller diameter of delivery catheter (3.5 French) compared to the original Beta-Cath system (5 French catheter). The new source/seed (3.5F source) has a different design from the original (5F) source. In this paper, we report the EGSnrc Monte Carlo results of two-dimensional dose rate distributions in water as well as the TG-60 dose parameters for the new 3.5F source and the original 5F source. A complete set of the dosimetric data for each individual seed is tabulated. A detailed dosimetric comparison was carried out for the two sources. The comparison shows that differences between the two sources are less than 5 in the region of interest for intravascular brachytherapy. Higher differences (up to 10) are seen in the near-source region, which is mainly inside the delivery catheter. Based on the present calculation and comparison, we conclude that the new Beta-Cath 3.5F system is dosimetrically equivalent to the original Beta-Cath (5F) system. Therefore, clinical dosimetry and the practice of using both the systems can be treated similarly.