We have investigated the molecular structure and two-photon absorption (2PA) properties relationship of two push–pull poly(fluorene) derivatives containing benzoselenadiazole and benzothiadiazole units. For that, we have used the femtosecond wavelength-tunable Z-scan technique with a low repetition rate (1 kHz) and an energy per pulse on the order of nJ. Our results show that both 2PA spectra present a strong 2PA (around 600 GM (1 GM = 1 × 10−50 cm4·s·photon−1)) band at around 720 nm (transition energy 3.45 eV) ascribed to the strongly 2PA-allowed 1Ag-like → mAg-like transition, characteristic of poly(fluorene) derivatives. Another 2PA band related to the intramolecular charge transfer was also observed at around 900 nm (transition energy 2.75 eV). In both 2PA bands, we found higher 2PA cross-section values for the poly(fluorene) containing benzothiadiazole unit. This outcome was explained through the higher charge redistribution at the excited state caused by the benzothiadiazole group as compared to the benzoselenadiazole and confirmed by means of solvatochromic Stokes shift measurements. To shed more light on these results, we employed the sum-over-states approach within the two-energy level model to estimate the maximum permanent dipole moment change related to the intramolecular charge transfer transition.