The transmission properties of a photonic crystal immersed in several different oils have been characterized using terahertz time domain spectroscopy in the spectral range of 0.3-1.5 THz. As in previous works, oil samples can be distinguished using terahertz transmission measurements. When the same oils are introduced into a photonic crystal, we find that the effective refractive index of the photonic crystal is sensitive to the properties of the oils and shows differences not seen in bulk measurements. These effects are described in detail and have potential applications in both the sensing of very small volumes of oils and in the fine control of the refractive indices of photonic crystals.