Calling displayTime(); without the prepended keyword 'this' is the main issue (line 16 below) as mentioned by GenericUser and Heretic Monkey in the comments above.

You probably already know this but you'll want to define a pauseTimer() method/function as well.

let endTimer = "0";
let isRunning = false;

//! CLASS
class Timer {
constructor(endTimer, isRunning) {
    this.endTimer = endTimer;
    this.isRunning = isRunning;
  }
}

Timer.prototype.startTimer = function() {
    if (this.endTimer === "0") {
        this.endTimer = new Date().getTime() + 1500000;
    }
    this.displayTime(); // this is the important line
    if (this.isRunning === true) {
        this.pauseTimer();
        this.isRunning
    }
    this.isRunning = true;
}

Timer.prototype.displayTime = function() {
    let now = new Date().getTime();
    let remainingTime = this.endTimer - now;
    let minutes = Math.floor(remainingTime / 1000 / 60);
    let seconds = Math.floor((remainingTime / 1000) % 60);
    if (seconds < 10) {
    seconds = "0" + seconds;
    }
    //timer.innerHTML = `<h1>${minutes}:${seconds}</h1>`;
    //start.textContent = "STOP"
    this.update = setInterval(this.displayTime, 100);
}

Timer.prototype.pauseTimer = function() {
    this.isRunning = false;
}

let newTimer = new Timer("0", true);
newTimer.startTimer();

//! EVENT LISTENERS

//start.addEventListener("click", newTimer.startTimer);

start.addEventListener("click", newTimer.startTimer.bind(newTimer));

class Timer {
    startTimer() {
        // You forgot this keyword
        this.displayTime();
    }
    displayTime() {
        console.log('do something');
    }

}

let newTimer = new Timer();

// addEventListener changes the context of this.
// Using an arrow function will keep 'this' keyword in tact inside startTimer method 
start.addEventListener('click', () => newTimer.startTimer)