A pair of isomeric chromophores based on the skeleton of bisarylacetylene using functionalized pyrazinoindenocarbazole moieties as the aryl substituents has been synthesized and characterized for their two- and three-photon-related properties in the femtosecond and nanosecond regimes. Our experiments have found that both model fluorophores manifest strong two-photon absorption in the near infrared region with one of the isomers exhibiting superior maximum two-photon absorptivity. It is realized that both the isomeric forms of functionalized pyrazinoindenocarbazoles are useful π-units for the construction of highly two-photon active materials but the effectiveness of the units is unequal, which is probably attributed to the difference of their conjugated structures. Two-photon-based optical power-limiting and stabilization against nanosecond laser pulses of one isomer was demonstrated. Additionally, these two chromophores exhibit strong three-photon-induced fluorescence when excited by the nanosecond laser with longer wavelengths (≥1000 nm), implying their potential utility to serve as prototypes for the development of three-photon materials.