fopFactory.setUserConfig(new File("path/to/config.xml"));

fopFactory.getFontManager().setFontBaseURL(fontBase);

<dependency>
    <groupId>org.apache.xmlgraphics</groupId>
    <artifactId>fop</artifactId>
    <version>2.1</version>
</dependency>

// setup xml input source
    String xml = object.toXml();
    StreamSource xmlSource = new StreamSource(new ByteArrayInputStream(xml.getBytes("UTF-8")));

    // setup xsl stylesheet source
    File xslFile = new File(stylesheetPath);
    FileInputStream xslFileStream = new FileInputStream(xslFile);
    StreamSource xslSource = new StreamSource(xslFileStream);

    // get transformer
    TransformerFactory tfactory = TransformerFactory.newInstance();
    Transformer transformer = tfactory.newTransformer(xslSource);

    // setup FOP
    FopFactory fopFactory = FopFactory.newInstance(xslFile);
    FOUserAgent foUserAgent = fopFactory.newFOUserAgent();
    foUserAgent.setProducer(this.getClass().getName());
    Fop fop = fopFactory.newFop(MimeConstants.MIME_PDF, foUserAgent, pdfContent);

    // perform transformation
    Result res = new SAXResult(fop.getDefaultHandler());
    transformer.transform(xmlSource, res);