Two independent chiral pool syntheses of both enantiomers of the TRPML inhibitor, trans‐ML‐SI3, were developed, starting from commercially available (1S,2R)‐ and (1R,2S)‐configured cis‐2‐aminocyclohexanols. Both routes lead to the target compounds in excellent enantiomeric purity and good overall yields. For the most attractive (−)‐trans‐enantiomer, the R,R‐configuration was identified by these unambiguous syntheses, and the results were confirmed by single‐crystal X‐ray structure analysis. These effective synthetic approaches further allow flexible variation of prominent residues in ML‐SI3 for future in‐depth analysis of structure–activity relationships as both the piperazine and the N‐sulfonyl residues are introduced into the molecule at late stages of the synthesis.