The aim of this clinical study was to compare dimensional changes of the transplanted grafts when the recipient area was prepared with either erbium:yttrium, aluminum, and garnet (Er:YAG) laser or scalpel in free gingival grafts (FGGs). In the first and second groups of ten patients, the recipient area was prepared with an Er:YAG laser and a scalpel, respectively. All grafts were harvested from the palate at standard dimensions (horizontal, 14 mm; vertical, 8 mm). Probing depth, clinical attachment level, and keratinized tissue width were measured before surgery. FGG dimensions (width, length, and area) were measured using the University of North Carolina-15 manual probe (N15) (Nordent Manufacturing, Inc., IL, USA) during surgery and at 10, 21, and 90 days postoperatively. Differences between the two groups were statistically analyzed. In both groups, there was a statistically significant reduction in vertical and horizontal dimensions (p < 0.05) and graft area (p < 0.05) at all time points compared to the baseline measurements. There were no significant differences between the two groups with respect to vertical and horizontal dimensions and graft area at day 90 (p > 0.05). The Er:YAG laser may be used with similar effectiveness as the scalpel in the preparation of the recipient site for free gingival grafts.