Abstract We investigate the impact of field-to-field variation, deriving from cosmic variance, in measured Ly α emitter (LAE) luminosity functions (LFs) and this variation’s impact on inferences of the neutral fraction of the intergalactic medium (IGM) during reionization. We post-process a z = 7 IGM simulation to populate the dark matter halos with LAEs. These LAEs have realistic UV magnitudes, Ly α fluxes, and Ly α line profiles. We calculate the attenuation of Ly α emission in universes with varying IGM neutral fraction, x ¯ H I . In a x ¯ H I = 0.3 simulation, we perform 100 realizations of a mock 2 deg 2  survey with a redshift window Δ z = 0.5 and flux limit f Ly α > 1 × 10 −17 erg s −1 cm −2 ; such a survey is typical in depth and volume of the largest LAE surveys conducted today. For each realization, we compute the LAE LF and use it to recover the input x ¯ H I . Comparing the inferred values of x ¯ H I across the ensemble of the surveys, we find that cosmic variance, deriving from large-scale structure and variation in the neutral gas along the sightline, imposes a floor in the uncertainty of Δ x ¯ H I ∼ 0.2 when x ¯ H I = 0.3. We explore mitigation strategies to decrease this uncertainty, such as increasing the volume, decreasing the flux limit, or probing the volume with many independent fields. Increasing the area and/or depth of the survey does not mitigate the uncertainty, but composing a survey with many independent fields is effective. This finding highlights the best strategy for LAE surveys aiming at constraining the x ¯ H I of the universe during reionization.