A series of (2,4-dihydroxybenzaldehyde dibenzyl semicarbazone) perfluoroalkyl carboxylato copper(II) complexes, [CF3(CF2)nCO2(LH)Cu] (LH2 = 2,4-dihydroxybenzaldehyde dibenzyl semicarbazone; n = 0, 2, 4, 6; 1–4), and (2,4-dihydroxybenzaldehyde dibenzyl semicarbazone) pyridine copper(II) perfluoroalkyl carboxylates, [(LH)(py)Cu]+[CF3(CF2)nCO2]− (5–8) were synthesized. The lipophilicity of these compounds was determined by reverse-phase thin layer chromatography and correlated with their cytotoxicity towards MOLT-4 human leukaemia cells. Cytotoxicity is more strongly correlated with lipophilicity for the non-ionic compounds (1–4) than for the ionic compounds (5–8). Compounds 5–8 (IC50 2.8–3.8 μM) are generally more cytotoxic than compounds 1–4 (IC50 3.6–8.4 μM). They also exhibit slightly higher cytotoxicity than the parent anticancer compound [(LH)(py)Cu]+[NO3]− (IC50 4.15 μM), suggesting that it is possible to enhance the cytotoxicity of [(LH)(py)Cu]+[NO3]− by replacing nitrate with anions of higher lipophilicity. Attempts to synthesize the non-fluorinated analogue [(LH)(py)Cu]+[CH3CO2]− resulted in the formation of the deprotonated complex [L(py)Cu], whose structure was confirmed by X-ray crystallography. The structural parameters indicate that the deprotonation site is the hydrazonic nitrogen of the semicarbazone ligand.