Renal tubular acidosis (RTA) is a rare disorder that can be inherited or acquired, and results in an inability of the kidneys to maintain normal acid-base balance. We present a case of recurrent, severe hypokalaemia and rhabdomyolysis in a young woman who had an associated normal anion gap metabolic acidosis and was subsequently diagnosed with distal RTA associated with Hashimoto’s thyroiditis. Distal RTA associated with Hashimoto’s thyroiditis is rare and probably develops because of autoimmune-mediated mechanisms, causing an inability of the H+-ATPase pump in alpha-intercalated cells of the cortical collecting duct to secrete H+, with subsequent failure of urinary acidification. In this case, this hypothesis was supported by the exclusion of common genetic mutations associated with distal RTA. We illustrate that utilizing a systematic, physiology-based approach for challenging electrolyte and acid-base disorders enables identification of the root cause and underlying disease mechanisms.