Store-operated calcium (Ca²⁺) entry (SOCE) in skeletal muscle is rapidly activated across the tubular system during direct activation of Ca²⁺ release. The tubular system is the invagination of the plasma membrane that forms junctions with the sarcoplasmic reticulum (SR) where STIM1, Orai1 and ryanodine receptors are found. The physiological activation of SOCE in muscle is not defined, thus clouding its physiological role. Here we show that the magnitude of a phasic tubular system Ca²⁺ influx is dependent on SR Ca²⁺ depletion magnitude, and define this as SOCE. Consistent with SOCE, the influx was resistant to nifedipine and BayK8644, and silenced by inhibition of SR Ca²⁺ release during excitation. The SOCE transient was shaped by action potential frequency and SR Ca²⁺ pump activity. Our results show that SOCE in skeletal muscle acts as an immediate counter-flux to Ca²⁺ loss across the tubular system during excitation-contraction coupling.