Kane scored twice to lead Tottenham to a comprehensive 3-0 victory over Everton in the Premier League on Saturday.
The 24-year-old England international striker did not score in August but he was at the double on Merseyside as he celebrated his 100th goal for Tottenham.
Pochettino heaped praise on the Premier League's reigning Golden Boot winner, likening him to former Argentina team-mate Batistuta, who was the country's all-time leading scorer before Lionel Messi broke the record last year.
"Batistuta was a killer," Pochettino said. "Very strong mentality, very strong shot, great professional. You can compare.
"For me, OK, I put Batistuta there, " he said, raising one hand above the other, "and Harry there," with his other hand a little lower.
"But Harry can be better. He is a killer, Harry Kane. Look at the goals he scored the last years! Mental level? Yes. Absolutely [they are the same].
"Maybe they have different characteristics but I think he is in that level, with Batistuta."
Pochettino added: "I would put Harry Kane in with Batistuta. All that is happening to him he deserves. He is the protagonist of his life, and he deserves all the prize."