We investigate the influence of the transverse mode of the pump beam and the geometry of the pump–probe configuration on the femtosecond two-photon excitation transient absorption (TA) spectroscopy. Strong modulation of the transient TA dynamics may result from the multi-peak distribution of the transverse mode of the pump beam, the large pump beam size, and the large separation angle between the pump and the probe beams, which is sensitive to the pulse length. Quantitative characterization of this kind of spatial effect is of general importance for the correct interpretation of the photophysical mechanisms that can be revealed by the two-photon TA measurements.