Can you charge a motorcycle battery with a car battery charger?

Yes as long as it is the right voltage: a 6v battery needs a 6v charger; a 12v battery needs a 12v charger.

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If you can set the battery charger's output to give either a 6 or a 12 volt output, then you must always remember to set it to 6 volts if you want to use it to charge a 6 volt motorcycle car battery.