Sub-seasonally resolved and replicated coral Sr/Ca time series at Clipperton Atoll (10°18′N, 109°13′W) in the eastern Pacific are assessed as a sea surface temperature (SST) proxy in this region with small seasonal SST variability. The composite coral Sr/Ca time series is a partially replicated record of three live and one sub-modern colony of Porites lobata extending back to 1874. Large inter-colony coral Sr/Ca offsets equate to relative SST differences of 0.6 to 4.3 °C and limit the ability to reconstruct absolute SST changes. Moreover, the replication method revealed a 12-year section of growth in one colony where mean Sr/Ca was anomalously low (~ 1 °C higher SST) relative to the other colonies without evidence of diagenesis or other significant skeletal alterations. The presence of this anomalous interval supports the need for multi-coral Sr/Ca replication in specific sites or regions. The Clipperton Composite Sr/Ca anomaly record is significantly coherent (r = 0.71–0.76, p < 0.001) with gridded instrumental SSTs but with larger amplitude decadal variance that appears to more accurately represent actual SST variability at Clipperton. The amplitude of the secular warming trend during the last century at Clipperton is 0.3 to 0.6 °C larger (~ twice as large) than the trend in the poorly “ground-truthed” instrumental SST records for the region. The interannual and decadal variability in Clipperton coral Sr/Ca demonstrates strong coherence to the Pacific Decadal Oscillation and the El Niño/Southern Oscillation (ENSO) with reduced ENSO variability from 1920 to late 1930s and enhanced variability in the late twentieth century.