Court martial is a major aspect of administration of military justice. In Nigeria, courts martial set up by the Army, Navy and Air Force have had numerous problems in the last 24 years leading to upturning of majority of the judgments by appellate courts. Judgments of about 70 percent of court martial cases that were appealed against in Nigeria between 1990 and 2014 were upturned by appellate courts. This work discovered that the major reasons that made appellate courts to upturn the judgments were on grounds of lack of jurisdiction, non-observance of the principles of fair hearing and lack of diligent prosecution among others. The Nigerian Armed Forces have lost several officers and soldiers to dismissals from courts martial of which their dismissals and sentence of imprisonment were upturned many years after, when it was difficult to get them back to service. This equally led to wastage of several man-hours prosecuting such cases at high expense. These were equally accompanied by harsh comments from justices of appellate courts which in some instances ridiculed the military justice system in Nigeria. The research is therefore aimed at proving that between 1990 and 2014, most of the court martial judgments were upturned on appeal based on lack of jurisdiction, non observance of the principles of fair hearing and lack of diligent prosecution. The major objective is to ensure that courts martial follow the prescribed procedures during trials. The research found out that one of the major reasons that makes court martial presidents and members conduct the procedures of the court in ways contrary to what it should be is command influence. Command influence is the negative influence of some convening authorities which makes the members to do his bidding at the courts martial. As a way out of the problem, the research recommended the insulation of courts martial from command influence and ensuring that those whose avoidable actions caused the upturning of court martial judgments on appeal get to feel the consequence of their actions. The principal ways of insulating courts martial from command influence as identified by the research include the Nigerian Armed Forces keying into the housing scheme of the Federal Mortgage Bank of Nigeria to get a personal house for every officer at the rank of Major. The officers are to bear the cost of the houses but to pay gradually from commission. In this way, officers will have a house to retire to, early in their career, thereby reducing the retirement phobia that facilitates command influence. The work equally recommended a situation where court martial members do not get evaluation reports from convening officers of courts martial where they are members. In the final analysis, the researcher believes that if these measures are adopted, the upturning of judgments of courts martial by appellate courts in Nigeria will be reduced to the barest minimum.