Fibroblast growth factor (FGF)-9 plays an important role in wound healing. However, the effects of non-ablative laser treatment on the expression of FGF9 have not been fully investigated. Non-ablative 1064-nm quasi-long pulsed and Q-switched Nd:YAG laser treatments were delivered to hairless mice with and without a carbon photoenhancer. For histological and immunohistochemical analyses, sections were stained with hematoxylin and eosin as well as FGF9 antibody. Significantly, increased epidermal and dermal thickness was noted in mice treated with carbon photoenhancer-assisted quasi-long pulsed or Q-switched laser treatments compared to those treated without a carbon photoenhancer. Expression of FGF9 was observed in both the epidermis and dermis in all groups of mice during the healing process. Earlier and more pronounced expression of FGF9 was detected in mice treated with carbon photoenhancer-assisted quasi-long pulsed laser therapy. In addition, two peaks of pronounced FGF9 expression were observed, especially in mice that underwent carbon photoenhancer-assisted 1064-nm quasi-long pulsed Nd:YAG laser treatment. A carbon photoenhancer seems to enhance the effect of quasi-long pulsed and Q-switched Nd:YAG laser treatment. In addition, expression of FGF9 may play an important role in the healing process after laser treatments and could contribute to histometric changes.