Long-term stress on marine organisms from ocean acidification will differ between seasons. As atmospheric carbon dioxide (CO2) increases, so do seasonal variations of ocean CO2 partial pressure (pCO2), causing summer and winter long-term trends to diverge1,2,3,4,5. Trends may be further influenced by an unexplored factor—changes in the seasonal timing of pCO2. In Arctic Ocean surface waters, the observed timing is typified by a winter high and summer low6 because biological effects dominate thermal effects. Here we show that 27 Earth system models simulate similar timing under historical forcing but generally project that the summer low, relative to the annual mean, eventually becomes a high across much of the Arctic Ocean under mid-to-high-level CO2 emissions scenarios. Often the greater increase in summer pCO2, although gradual, abruptly inverses the chronological order of the annual high and low, a phenomenon not previously seen in climate-related variables. The main cause is the large summer sea surface warming7 from earlier retreat of seasonal sea ice8. Warming and changes in other drivers enhance this century’s increase in extreme summer pCO2 by 29 ± 9 per cent compared with no change in driver seasonalities. Thus the timing change worsens summer ocean acidification, which in turn may lower the tolerance of endemic marine organisms to increasing summer temperatures.