Pope John Paul II confirmed that animals do have a soul and that yes, they would be with us within Heaven. (Source) Many theologians, however, do not believe this to be the case. 
I decided to do some reading on this and was startled to find that opinions vary all across the board.
Theologians appear to pretty much disagree with the Pope, and feel that animals, while being living “souls” as we are, do not carry an immortal soul that lives on past death, as ours does.
Pet owners of all shapes and sizes disagree with the studied theologians; they feel that there can be no doubt that animals have souls.
As a lover of all animals and life, I tend to agree with the side of the aisle that feels that animals do have a soul, great intelligence and intuitiveness, and the ability to empathize. I’m not sure, however, that animals have a ‘spirit,’ which is the part of us that endures, that lives on eternally after acceptance of Jesus Christ and belief in who He is and what He did for us.
This topic can become complicated and the fact is that no one really knows for sure. I prefer to believe that animals will have the opportunity to live on, and that they will go to Heaven; that we will one day see our beloved pets again and live with them for all eternity. This is very important to me because of the great love I have for my pets, of which I have several. I choose to believe that my animals have a soul and a spirit, and pray I will see them again one day.
The research appears to only bring about greater speculation, as no one can be certain, it would seem.
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Question: “Do pets / animals go to Heaven? Do pets / animals have souls?”
Answer: The Bible does not give any explicit teaching on whether pets/animals have “souls” or whether pets/animals will be in heaven. However, we can use general biblical principles to develop some clarity on the subject. The Bible states that both man (Genesis 2:7) and animals (Genesis 1:30; 6:17; 7:15, 22) have the breath of life.
The primary difference between human beings and animals is that humanity is made in the image and likeness of God (Genesis 1:26-27), while animals are not. Being made in the image and likeness of God means that human beings are like God, capable of spirituality, with mind, emotion, and will, and they have a part of their being that continues after death. If pets/animals do have a “soul” or immaterial aspect, it must therefore be of a different and lesser “quality.” This difference possibly means that pet/animal “souls” do not continue in existence after death.
Another factor to consider is that animals are a part of God’s creative process in Genesis. God created the animals and said they were good (Genesis 1:25). Therefore, there is no reason why there could not be animals on the new earth (Revelation 21:1). There will most definitely be animals during the millennial kingdom (Isaiah 11:6; 65:25). It is impossible to say definitively whether some of these animals might be the pets we had while here on earth. We do know that God is just and that when we get to heaven we will find ourselves in complete agreement with His decision on this issue, whatever it may be.
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But does animal intelligence constitute a soul? Does a pet’s emotions and ability to relate to human beings mean that animals possess an immortal spirit that will survive after death?
Theologians say no. They point out that man was created superior to animals and that animals can’t be equal with him.
Then God said, “Let us make man in our image, in our likeness, and let them rule over the fish of the sea and the birds of the air, over the livestock, over all the earth, and over all the creatures that move along the ground.” (Genesis 1:26, NIV)
Most interpreters of the Bible assume that man’s likeness to God and animals’ subservience to man implies that animals may have the “breath of life,” nephesh in Hebrew, but not an immortal soul in the same sense as man’s.
Even so, the prophet Isaiah says God will include animals in the new heavens and new earth:
“The wolf and the lamb will feed together, and the lion will eat straw like the ox, but dust will be the serpent’s food. They will neither harm nor destroy on all my holy mountain, says the LORD.” (Isaiah 65: 25, NIV)
In the last book of the Bible, Revelation, the Apostle John’s vision of heaven also included animals, showing Christ and the armies of heaven “riding on white horses.” (Revelation 19:14, NIV) 
Most of us can’t picture a paradise of unspeakable beauty without flowers, trees, and animals. Would it be heaven for an avid birdwatcher if there are no birds? Would a fisherman want to spend eternity with no fish? And would it be heaven for a cowboy without horses?
While theologians may be stubborn in classifying animals’ “souls” as inferior to those of humans, those learned scholars must admit that descriptions of heaven in the Bible are sketchy at best. The Bible does not give a definitive answer on the question of whether we will see our pets in heaven, but it does say, “… with God, all things are possible.” (Matthew 19:26, NIV)
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Question: Do animals have a soul?
Answer: As a rule, the complete question involves concern about animals, especially pets, being in heaven.
The original creation.When we visit the original creation, we discover a number of truths. One apparent truth is the uniqueness of man compared to the lower animal creation. Only to man was it said, “Let us make man in our image, after our likeness….” (Gen. 1: 26). Animals are next mentioned in the verse, but from the standpoint of their subservience to man.
The fate of man and animals. The wise man had much to say regarding man, his birth, life, and destiny. He wrote, “Then shall the dust return to the earth as it was; and the spirit shall return unto God who gave it” (Eccl. 12: 7). Earlier, he wrote regarding man and the beast: “Who knoweth the spirit of man that goeth upward, and the spirit of the beast that goeth downward to the earth?” (Eccl. 3: 21.) This question is clearly answered in the above noted chapter twelve, verse seven.
Animals have a soul in the sense that they possess life.A common Hebrew word translated life (soul) is nephesh. Nephesh is used for the life or breath of both animals and man (Gen. 1: 20, 30; 19: 17). Life is that state that is the opposite of death. It is a state of animation, breathing, and awareness. Men and animals alike possess a soul in the sense of breath (nephesh). However, in the sense of possessing a part or element that lives forever, as man possesses, animals do not possess an eternal spirit (cp. Matt. 25: 46). The animal simply and totally returns to the dust, the spirit of man continues to exist (Eccl. 3: 21, cp. 12: 7).
The fact that animals do not possess an eternal soul in the sense that man does, does not de-emphasize their value as companions to man. Pets can and do become an important part in the lives of millions. Also, in man’s charge over the animal kingdom, it behooves man to protect and not abuse the animals (Gen. 1: 26-28).
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And one more in depth reading with a variety of opinion upon it, many stating that yes, animals do have souls.
Source
- Soul & Spirit (lifeofafemalebiblewarrior.wordpress.com)
- Souls Awakened: The Animals Who Have Shaped Us (bipedsandbrutes.wordpress.com)
What Do You Think? Courteous Opinion Always Welcome!
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