diff --git a/build.gradle b/build.gradle
index e8d6177fe4..8e45f1acdc 100644
--- a/build.gradle
+++ b/build.gradle
@@ -34,6 +34,7 @@ dependencies {
     implementation  group: 'org.apache.commons', name: 'commons-csv', version: '1.6'
     implementation group: 'org.apache.commons', name: 'commons-text', version: '1.9'
     implementation  group: 'org.fusesource.jansi', name: 'jansi', version: '1.18'
+    implementation  group: 'org.eclipse.jgit', name: 'org.eclipse.jgit', version: '5.9.0.202009080501-r'
 
     testImplementation group: 'junit', name: 'junit', version: '4.12'
 }
diff --git a/src/main/java/reposense/git/GitBranch.java b/src/main/java/reposense/git/GitBranch.java
index 7f70fa1a57..c7ea7da6ab 100644
--- a/src/main/java/reposense/git/GitBranch.java
+++ b/src/main/java/reposense/git/GitBranch.java
@@ -1,30 +1,45 @@
 package reposense.git;
 
-import static reposense.system.CommandRunner.runCommand;
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
 
-import java.nio.file.Path;
-import java.nio.file.Paths;
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.lib.Ref;
 
 import reposense.git.exception.GitBranchException;
-import reposense.util.StringsUtil;
+import reposense.system.LogsManager;
 
 /**
  * Contains git branch related functionalities.
  * Git branch is responsible for list, create, or delete branches.
  */
 public class GitBranch {
+    private static final Logger logger = LogsManager.getLogger(GitBranch.class);
+    private static final String MESSAGE_MISSING_REPOSITORY =
+            "The directory %s does not exist or is not a Git repository.";
 
     /**
      * Returns the current working branch of the repository at {@code root}.
      */
     public static String getCurrentBranch(String root) throws GitBranchException {
-        Path rootPath = Paths.get(root);
-        String gitBranchCommand = "git branch";
+        String branch;
 
         try {
-            return StringsUtil.filterText(runCommand(rootPath, gitBranchCommand), "\\* (.*)").split("\\*")[1].trim();
-        } catch (RuntimeException rte) {
-            throw new GitBranchException(rte);
+            Git git = Git.open(new File(root));
+            List<Ref> gitRefs = git.getRepository().getRefDatabase().getRefs();
+
+            if (gitRefs.size() == 0) {
+                // An empty repository does not have any refs
+                return null;
+            }
+
+            return git.getRepository().getBranch();
+        } catch (IOException ioe) {
+            logger.log(Level.SEVERE, String.format(MESSAGE_MISSING_REPOSITORY, root), ioe);
+            throw new GitBranchException(ioe);
         }
     }
 }
diff --git a/src/main/java/reposense/report/RepoCloner.java b/src/main/java/reposense/report/RepoCloner.java
index 2ccf0a998f..35e9a7d240 100644
--- a/src/main/java/reposense/report/RepoCloner.java
+++ b/src/main/java/reposense/report/RepoCloner.java
@@ -68,11 +68,18 @@ public RepoLocation getClonedRepoLocation() {
             String bareRepoPath = FileUtil.getBareRepoPath(configs[currentIndex]).toString();
             currentRepoDefaultBranch = GitBranch.getCurrentBranch(bareRepoPath);
         } catch (GitBranchException gbe) {
-            // GitBranch will throw this exception when repository is empty
             logger.log(Level.WARNING, String.format(MESSAGE_ERROR_GETTING_BRANCH,
                     configs[currentIndex].getLocation(), configs[currentIndex].getBranch()), gbe);
             return null;
         }
+
+        if (currentRepoDefaultBranch == null) {
+            // Current repository is empty
+            logger.log(Level.WARNING, String.format(MESSAGE_ERROR_GETTING_BRANCH,
+                    configs[currentIndex].getLocation(), configs[currentIndex].getBranch()));
+            return null;
+        }
+
         cleanupPrevRepoFolder();
 
         previousIndex = currentIndex;