Verb tense is the difference. Examples: The time has come for me to tend to my kids for the day (current). The time had come to take the pizza out of the oven to eat it. (past)

The only difference is the tense or time that the situation takes place. "The time has come" is used for describing the situation taking place in the present. "The time had come" is when someone is describing the situation in the past or when the context of the situation is in past tense.