Gene flow, through allele migration and spread, is critical in determining patterns of population genetic structure, divergence and local adaptation. While evolutionary theory has typically envisioned gene flow as a continuous connection among populations, many processes can render it fluctuating and intermittent. We analyze mathematically a stochastic mainland-island model in continuous time, in which migration occur as recurrent “pulses”. We derive simple analytical approximations regarding how migration pulsedness affects the effective migration rates across a range of selection and dominance scenarios. Predictions are validated with stochastic simulations and summarized with graphical interpretations in terms of fixation probabilities. We show that migration pulsedness can decrease or increase gene flow, respectively above or below a selection threshold that is for additive alleles and lower for recessive deleterious alleles. We propose that pulsedness may leave a genomic detectable signature, by differentially affecting the fixation rates of loci subjected to different selection regimes. The additional migration created by pulsedness is called a “pulsedness” load. Our results indicate that migration pulsedness, and more broadly temporally variable migration, is important to consider for evolutionary and population genetics predictions. Specifically, it would overall be detrimental to the local adaptation and persistence of small peripheral populations.