Together with his brother Rabbi Avraham, Rabbi Refael was orphaned from his illustrious father Rabbi Shmuel when the latter passed away in the prime of his life of twenty-one years.
Rabbi Refael was a mere three-year-old, while his brother was only two. They were brought up by their paternal grandfather, the parnas Rabbi Moshe.
In time, the two were to become great luminaries who enlightened the Torah world with their valuable seforim. Rabbi Refael's seforim were: the Pri Ha'adamah on the Rambam, Droshos Pnei Ha'adamah, Sheilos Uteshuvos Mizbeiach Adamah, Ittur Bikkurim and Minchas Bikkurim, the latter two being chidushim on Shas in halochoh and aggadah. His brother Rabbi Avraham authored the seforim Sheilos Uteshuvos Sdei Ha'aretz, Diglo Ahavah and Siach Hassadeh.
Already at the age of six, Refael went to the beis medrash of the wealthy Rabbi Yisrael Yaakov Firirah o"h, where the cream of talmidei chachomim sat and learned from daybreak until late at night. The young orphan too, never missed a day of rising at the crack of dawn to learn.
In his sefer Megillas Yuchasin in the kuntrus Megillas Haneis, Rabbeinu describes in detail the phenomenal miracles that occurred to him when he left Egypt for Eretz Yisroel, through the Sinai desert.
"It was midday, when I was suddenly accosted by nine formidable-looking men with swords drawn in their hands. The first thing they did was kill the ass upon which I was riding and then they turned to me. They commanded me to remove my clothing and confiscated all my belongings. I was left empty-handed, my whole body trembling in fear, and only covered by a shirt and tzitzis.
I accepted mentally the Heavenly decree and thought to myself that just as I was born bare and naked, now too I would return to Yerushalayim with no physical belongings. I began to try and reckon which was the best way out of the wilderness in the direction of the Holy Land, but before I knew it, the bandits were fast approaching me again, swords drawn and shouting their warlike cries. They fell upon me, striking me murderously and injuring me, until I fell to the ground.
I readied myself for what I was sure was my imminent death and started saying Shema Yisrael, having in mind kabolas ol malchus Shomayim.
Just then, one of the gang stood over me and began hitting me on the neck with his sword. However, Hashem was with me; in the merit of my holy ancestors, and that of Yerushalayim ir hakodesh, the sword broke into two!
His friend was quick to take over where he had left off. With a wickedness that was surpassed only by his anger, he too brought down his sword on my neck. Again the neis happened and his sword split in half.
As each of the nine took their turn, my neck seemed to have turned into marble. I felt no pain and each of their swords were broken.
The men were astonished and afraid; such a thing had never happened to them. They fled to a distance of two miles, leaving me alone without a clue as to what to do or where to escape.
After distancing themselves two miles from me, the reshoim returned, subdued and contrite. They admitted that they were still trembling in fear after their experience, and could not continue on their way. They had decided to come back together to beg my forgiveness, and to return all my belongings.
Having done so, they were off, and I began to breathe more freely. At that moment I promised that I and my children would observe this date — the sixteenth of Adar — as a day of feasting, rejoicing, and praise-giving to Hashem, for sparing my life with such openly-manifest miracles.
At the end of the booklet, Rabbi Refael adds yet another neis that he merited to experience.
"After the bandits left me I remained on the spot wondering where to turn and how I would reach Yerushalayim.
"A while passed and then a man appeared to me, his face aflame with holiness.
"`Where are you going?' he asked me.
"`My master,' I answered, `my only will and ardent desire is to go to the holy city Yerushalayim.'
"Gently, he assured me, `I will show you the way, have no fear.'
"Within a minute we arrived at Yerushalayim ir hakodesh."
Rabbi Refael concludes with a tefilloh that he merit to greet Moshiach with the building of the Beis Hamikdash.
In Yerushalayim, Rabbeinu was chosen to serve as Rishon Letzion, a position from which he set many takonos in the holy city.
A by now famous takonoh, that was kept up until the War of Independence in 1948, was that an unmarried boy over the age of twenty should not lodge overnight in Yerushalayim. This was to prevent the problem of bochurim growing too old. With this psak they would get married between eighteen and twenty, which was Rabbeinu's intention.
The motive behind his takonos was often to strengthen the laws of tznius. For example he decried the sitting of women at the entrances to their courtyards.
Another was, that a woman should not go to daven in shul for mincha and ma'ariv until the age of forty, apart from on Rosh Hashonoh and Yom Kippur.
It is well worth noticing that the other geonim of his time agreed and gave their signatures to these takonos. Among them were HaRav Yonah Navon, HaRav Yitzchak Zerachya Azulai and HaRav Yisroel Yitzchak Algazi.
In praise of Yerushalayim, Rabbeinu explains in his sefer Pri Ha'adamah why a taanis tzibbur is never decreed in the holy city at the time of an earthquake.
"We have a kabalah in Toras Hanistar that it has never in the past been heard of, and neither will it in the future, that a person was or will be caused bodily harm in Yerushalayim due to an earthquake or landslide. As it says in Tehillim (147:13), `For He strengthened the bars of your gates, (and) blessed your sons in your midst.'
"The very nature of Yerushalayim is that her inhabitants are blessed and will not be killed by an earthquake or landslide."
He brings here the example of the earthquake that took place in 5520/1760 in Eretz Yisroel. At the time, one hundred and sixty two Jewish lives were lost R"l in Tzfas, whereas in Yerushalayim there was not one casualty. A day of crying and mourning was decreed, but not a ta'anis tzibbur.