The association of the V-prep and a resin-modified glass ionomer cement (RMGIC) has shown to be a suitable alternative for the orthodontic bracket bonding procedure in vitro. The aim of this study was to evaluate over eighteen months the clinical bonding failure and survival rates of the conventional bonding technique using the Transbond XT (3M Unitek, Monrovia, CA, USA) and the RMGIC Fuji Ortho LC (GC Corporation, Tokyo, Japan) prepared with the V-prep. Therefore, one operator using the straight-wire technique bonded two hundred metallic brackets to upper and lower premolars of twenty-five patients requiring an orthodontic treatment. The randomized trial was a single-blind design in a split-mouth comparison. Each patient was randomly allocated one of the two bonding systems for each premolar on each side of the mouth. The bonding and rebonding techniques were standardized throughout the trial and bond failure was recorded each month for a period of eighteen months. The survival rates of the brackets were estimated by Kaplan–Meier and log-rank test (p < 0.05). A total of 200 orthodontic brackets were included in the study with a significant lower failure rate of 9.0% for the V-prep and RMGIC compared to 25.0% for the conventional bonding technique (p < 0.05). A higher survival rate was observed for the V-prep and RMGIC (16.36 months) over the conventional bonding technique (13.95 months) (p < 0.05). Lower premolar bonding failure was higher than upper premolar for both bonding techniques. The V-prep followed by RMGIC, with enamel surface protection abilities, can be used as an alternative bonding technique in an orthodontic treatment.