Main.java

package ru.varren;

import javafx.application.Application;
import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.concurrent.Worker;
import javafx.scene.Scene;
import javafx.scene.control.Button;
import javafx.scene.control.TextField;
import javafx.scene.layout.VBox;
import javafx.scene.web.WebEngine;
import javafx.scene.web.WebView;
import javafx.stage.Stage;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;

import java.io.File;
import java.io.IOException;
import java.util.Scanner;

public class Main extends Application{
    public static void main(String[] args) {
        launch(args);
 
    }


    public void start(Stage primaryStage) throws Exception {
        VBox root = new VBox();
        final WebView webView = new WebView();
        webView.getEngine().getLoadWorker().stateProperty().addListener(
                new ChangeListener<Worker.State>() {
                    public void changed(ObservableValue ov, Worker.State oldState, Worker.State newState) {
                        if (newState == Worker.State.SUCCEEDED) {
                            try {
                                WebEngine engine = webView.getEngine();

                                String highlightScript = readFile(Main.class.getResource("/script.js").getPath());
                                Document page = engine.getDocument();

                                Element jquery =  page.createElement("script");
                                jquery.setAttribute("src",Main.class.getResource("/jquery-1.11.3.min.js".getPath());

                                Element jqueryHighlight =  page.createElement("script");
                                jqueryHighlight.setTextContent(highlightScript);

                                Node head =  page.getElementsByTagName("head").item(0);
                                head.appendChild(jquery);
                                head.appendChild(jqueryHighlight);
                            } catch (IOException e) {
                                e.printStackTrace();
                            }
                        }
                    }
                });

        webView.getEngine().load("http://stackoverflow.com/questions/30767692/cant-get-javascript-to-work-in-webview");
        
        TextField textField = new TextField();
        textField.setText("test");
        
        Button button = new Button("Test Javascript");
        button.setOnMouseClicked(e->{
            webView.getEngine().executeScript("$('body').removeHighlight().highlight('" + textField.getText() + "')");
            System.out.println("click");
        });

        root.getChildren().addAll(webView,textField,button);

        Scene scene = new Scene(root,600,600);
        primaryStage.setScene(scene);
        primaryStage.show();
    }

    private String readFile(String pathname) throws IOException {

        File file = new File(pathname);
        StringBuilder fileContents = new StringBuilder((int)file.length());
        String lineSeparator = System.getProperty("line.separator");

        try (Scanner scanner = new Scanner(file)) {
            while (scanner.hasNextLine()) {
                fileContents.append(scanner.nextLine()).append(lineSeparator);
            }
            return fileContents.toString();
        }
    }

}

script.js

/*

 highlight v5

 Highlights arbitrary terms.

 <http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html>

 MIT license.

 Johann Burkard
 <http://johannburkard.de>
 <mailto:jb@eaio.com>

 */

jQuery.fn.highlight = function(pat) {
    function innerHighlight(node, pat) {
        var skip = 0;
        if (node.nodeType == 3) {
            var pos = node.data.toUpperCase().indexOf(pat);
            pos -= (node.data.substr(0, pos).toUpperCase().length - node.data.substr(0, pos).length);
            if (pos >= 0) {
                var spannode = document.createElement('span');
                spannode.className = 'highlight';
                var middlebit = node.splitText(pos);
                var endbit = middlebit.splitText(pat.length);
                var middleclone = middlebit.cloneNode(true);
                spannode.appendChild(middleclone);
                middlebit.parentNode.replaceChild(spannode, middlebit);
                skip = 1;
            }
        }
        else if (node.nodeType == 1 && node.childNodes && !/(script|style)/i.test(node.tagName)) {
            for (var i = 0; i < node.childNodes.length; ++i) {
                i += innerHighlight(node.childNodes[i], pat);
            }
        }
        return skip;
    }
    return this.length && pat && pat.length ? this.each(function() {
        innerHighlight(this, pat.toUpperCase());
    }) : this;
};

jQuery.fn.removeHighlight = function() {
    return this.find("span.highlight").each(function() {
        this.parentNode.firstChild.nodeName;
        with (this.parentNode) {
            replaceChild(this.firstChild, this);
            normalize();
        }
    }).end();
};