Microneedle systems have gained attention as having many advantages over transdermal patches and hypodermic needles. The procedure provides adequate skin permeation rates without pain or severe infection. To obtain information for designing a microneedle system, macroneedles were used instead of microneedles to investigate the effects of pretreatment of needle puncture in the skin barrier stratum corneum on in vitro skin permeation of fluorescein isothiocyanate (FITC)-dextrans (4.3, 9.6 and 42.0 kDa) (FD-4, FD-10 and FD-40). The effect of sandpaper abrasion was also investigated for comparison. Both pretreatments on the skin barrier significantly increased the skin permeation of FDs. Lactate dehydrogenase (LDH) leaching was measured after pretreatment of macroneedle and sandpaper abrasion on the skin to evaluate the skin damage by these pretreatment methods. Lower leaching of LDH was observed after macroneedle puncture than after sandpaper abrasion. Next, a parallel permeation-resistance model of the skin barrier was established. Skin permeation of FD-10 was predicted by the model as a function of the number of pores in the skin barrier. Our results suggest that needle puncture may provide a safe, efficient and controllable alternative for increasing transdermal drug delivery.