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Ningaloo Niño/Niña is a mode of climate variability in the southeastern Indian Ocean with huge impacts on Australian climate. El Niño‐Southern Oscillation (ENSO), as the dominant remote forcing, triggers Ningaloo Niño/Niña. However, how this teleconnection will respond to greenhouse warming is unclear. Using Coupled Model Intercomparison Project phase 5 (CMIP5) multi‐model simulations, we find a weakened ENSO‐Ningaloo Niño/Niña teleconnection under greenhouse warming, which manifests as weakened atmospheric teleconnection from La Niña to Ningaloo Niño. Such weakened teleconnection can be linked to the tropical Pacific mean state changes including an El Niño‐like warming pattern and more stable atmosphere in the future climate, both suppressing the atmospheric convection in the western tropical Pacific, leading to a weaker Matsuno‐Gill response in the southeastern Indian Ocean. Our results suggest that Ningaloo Niño/Niña becomes more challenging to predict as greenhouse warming continues.