In this work we consider lightcone fluctuation effects in a five-dimensional spacetime arising as a consequence of the compactification of the extra dimension via a quasiperiodic condition, characterized by a phase angle 2πα. By considering light propagating in a non-compactified direction we are able to compute both the renormalized graviton two-point function and the flight time of a photon caused by the fluctuations. We show that the resulting expressions depend on the quasiperiodic parameter, the compactification length and also on the distance traveled by the photon. Based on the Near-Infrared Spectrograph (NIRSpec) sensitivity built on the James Webb Space Telescope, we discuss the possibility of making estimations on the size of the extra dimension if one assumes that the mean deviation on the flight time of photons can be observed through the NIRSpec. We also analyze the differences between the estimations in the periodic α = 0, antiperiodic α = 1/2 and other condition cases for α.