Wavelet analysis (WA) decomposes laser Doppler (LD) microcirculatory signals into characteristic frequency intervals related to endothelial nitric oxide (NO)-independent, endothelial NO-dependent, neurogenic, myogenic, respiratory, and cardiac physiological influences. Since LD signals have a finite length, the WA results suffer from spectral leakage due to edge effects. The cone of influence (COI) delineates the regions of the wavelet scalogram where these effects become important. We aimed to determine whether accounting for the COI leads to significant differences in the WA results. Two typical patterns of LD signals were analysed: a baseline and a post-occlusive reactive hyperemia (PORH) signal. The WA spectra were constructed without and with excluding data affected by the COI. The relative power (RP = median power of each frequency interval/median power of the total spectrum) of the spectral components obtained without and with the COI was compared. Applying the COI correction did not significantly affect the baseline signals. On the contrary, in PORH, accounting for the COI resulted in significant differences in the RP of the endothelial NO-independent (p = 0.0005; Wilcoxon signed-rank test), endothelial NO-dependent (p = 0.0005), neurogenic (p = 0.0038), myogenic (p = 0.001), respiratory (p = 0.0002), and cardiac frequency bands (p = 0.0002). The results suggest that applying the COI correction to the WA results obtained from the LD signals is desirable, especially for transient signals.