The question was not specific in the period of time to which it refers, as there was more than one English Civil War. Any thorough answer, however, would have to expand beyond the limited timeframes of the civil wars in order to provide the proper degree of context. That caveat aside, the period during which many historians place the “English Civil War” is between 1642 and 1649, so what follows will emphasize that period.
Jewish existence in England has been dated to the mid-11th Century, with a settlement in Oxfordshire providing the first documented presence of Jews in England. During many of the first several hundred years of Jewish life in England, they were both ostracized and protected by the series of monarchs who ruled that country. England, of course, was overwhelmingly Christian, and the small Jewish minority fell under the direct protection of the kings, who regularly exacted tribute in exchange. Jews in England generally prospered as businessmen and were often approached by Christian noblemen and knights for financial assistance. While England’s Jews enjoyed a certain level of protection, however, the initiation of the Crusades in 1096. Massacres of Jews would subsequently become a prominent feature of religious-based warfare for hundreds of years.
Despite the massacres, Jews continued to be protected by most of the kings who reigned during the medieval period. As with the start of the Crusades, however, a new development during the 12th Century presaged a permanent fixture of anti-Semitic violence: the blood libel. Dated to a hoax in 1144, the rumor that Jews ritually killed Christian children and drank their blood as part of a religious ritual took hold and precipitated the wide-spread killing of Jews throughout England and, eventually, continental Europe. The Jewish experience in England would remain this way for hundreds more years, with protection provided by the kings alternating with spasms of anti-Semitic violence. The nadir of Jewish life in England began under the reign of Edward I (1272-1307), with the king imposing unprecedented restrictions on Jewish life and eventually expelling the Jewish population from England, an expulsion that would remain in effect until the 17th Century Civil War, during which the execution of Charles I in 1649 resulted in the reversal of the edict expelling the Jews.
The return of the Jews to England was welcomed by Oliver Cromwell as beneficial to the war-ravaged country’s economy, as well as to the notion that the return of the Messiah could only occur if Jews were present far and wide. The answer to the question, then, is that, during the first years of the Civil War, the Jews were essentially non-existent in England (although a very small population had remained in parts of the country). As the English Crown hostile to the presence of Jews suffered setbacks, however, and especially after Cromwell’s ascendance, Jews once again enjoyed protection from England’s rulers, although pre-expulsion numbers were never reestablished.